scholarly journals The Evolutionary and Historical Foundation of the Modern Horse: Lessons from Ancient Genomics

2020 ◽  
Vol 54 (1) ◽  
pp. 563-581
Author(s):  
Ludovic Orlando
Keyword(s):  
Ancient Dna ◽  
Evolutionary History ◽  
Economic Value ◽  
Domestic Horse ◽  
Human History ◽  
Archaeological Remains ◽  
Animal Kingdom ◽  
Sequencing Technologies ◽  
Sport Industry ◽  
Horse Domestication

The domestication of the horse some 5,500 years ago followed those of dogs, sheep, goats, cattle, and pigs by ∼2,500–10,000 years. By providing fast transportation and transforming warfare, the horse had an impact on human history with no equivalent in the animal kingdom. Even though the equine sport industry has considerable economic value today, the evolutionary history underlying the emergence of the modern domestic horse remains contentious. In the last decade, novel sequencing technologies have revolutionized our capacity to sequence the complete genome of organisms, including from archaeological remains. Applied to horses, these technologies have provided unprecedented levels of information and have considerably changed models of horse domestication. This review illustrates how ancient DNA, especially ancient genomes, has inspired researchers to rethink the process by which horses were first domesticated and then diversified into a variety of breeds showing a range of traits that are useful to humans.

scholarly journals Looking Backward To Move Forward: the Utility of Sequencing Historical Bacterial Genomes

2019 ◽  
Vol 57 (8) ◽  
Author(s):  
Rebecca J. Bennett ◽  
Kate S. Baker
Keyword(s):  
Ancient Dna ◽  
Culture Collection ◽  
Health Concern ◽  
Human History ◽  
Bacterial Genomes ◽  
Content Type ◽  
Retrospective Diagnosis ◽  
Sequencing Technologies ◽  
Sequencing Studies ◽  
Unique Source

ABSTRACT Many pathogens that caused devastating disease throughout human history, such as Yersinia pestis, Mycobacterium tuberculosis, and Mycobacterium leprae, remain problematic today. Historical bacterial genomes represent a unique source of genetic information and advancements in sequencing technologies have allowed unprecedented insights from this previously understudied resource. This minireview brings together example studies which have utilized ancient DNA, individual historical isolates (both extant and dead) and collections of historical isolates. The studies span human history and highlight the contribution that sequencing and analysis of historical bacterial genomes have made to a wide variety of fields. From providing retrospective diagnosis, to uncovering epidemiological pathways and characterizing genetic diversity, there is clear evidence for the utility of historical isolate studies in understanding disease today. Studies utilizing historical isolate collections, such as those from the National Collection of Type Cultures, the American Type Culture Collection, and the Institut Pasteur, offer enhanced insight since they typically span a wide time period encompassing important historical events and are useful for the investigating the phylodynamics of pathogens. Furthermore, historical sequencing studies are particularly useful for looking into the evolution of antimicrobial resistance, a major public health concern. In summary, although there are limitations to working with historical bacterial isolates, especially when utilizing ancient DNA, continued improvement in molecular and sequencing technologies and the resourcefulness of investigators mean this area of study will continue to expand and contribute to the understanding of pathogens.

scholarly journals Ancient DNA set to rewrite human history

Nature ◽  
2010 ◽  
Vol 465 (7295) ◽  
pp. 148-148 ◽  
Author(s):  
Rex Dalton
Keyword(s):  
Ancient Dna ◽  
Human History

scholarly journals Significance of the Diversification of Wheat Species for the Assembly and Functioning of the Root-Associated Microbiome

2022 ◽  
Vol 12 ◽  
Author(s):  
Cécile Gruet ◽  
Daniel Muller ◽  
Yvan Moënne-Loccoz
Keyword(s):  
Mycorrhizal Fungi ◽  
Evolutionary History ◽  
Large Body ◽  
Taxonomic Diversity ◽  
Wheat Root ◽  
Wheat Species ◽  
Sequencing Technologies ◽  
The World ◽  
Baseline Information ◽  
Microbe Interactions

Wheat, one of the major crops in the world, has had a complex history that includes genomic hybridizations between Triticum and Aegilops species and several domestication events, which resulted in various wild and domesticated species (especially Triticum aestivum and Triticum durum), many of them still existing today. The large body of information available on wheat-microbe interactions, however, was mostly obtained without considering the importance of wheat evolutionary history and its consequences for wheat microbial ecology. This review addresses our current understanding of the microbiome of wheat root and rhizosphere in light of the information available on pre- and post-domestication wheat history, including differences between wild and domesticated wheats, ancient and modern types of cultivars as well as individual cultivars within a given wheat species. This analysis highlighted two major trends. First, most data deal with the taxonomic diversity rather than the microbial functioning of root-associated wheat microbiota, with so far a bias toward bacteria and mycorrhizal fungi that will progressively attenuate thanks to the inclusion of markers encompassing other micro-eukaryotes and archaea. Second, the comparison of wheat genotypes has mostly focused on the comparison of T. aestivum cultivars, sometimes with little consideration for their particular genetic and physiological traits. It is expected that the development of current sequencing technologies will enable to revisit the diversity of the wheat microbiome. This will provide a renewed opportunity to better understand the significance of wheat evolutionary history, and also to obtain the baseline information needed to develop microbiome-based breeding strategies for sustainable wheat farming.

scholarly journals Genome sequencing in plants and the genus Panax L.

2016 ◽  
Vol 14 (1) ◽  
pp. 1-13
Author(s):  
Lê Thị Thu Hiền ◽  
Hugo De Boer ◽  
Vincent Manzanilla ◽  
Hà Văn Huân ◽  
Nông Văn Hải
Keyword(s):  
Development Strategy ◽  
Genome Sequencing ◽  
Evolutionary History ◽  
Applied Research ◽  
Plant Genome ◽  
Related Genome ◽  
Genetic Characteristics ◽  
Biochemical Pathways ◽  
Sequencing Technologies ◽  
Herbal Plants

Advances in genome sequencing technologies have created a new genomic era of life sciences research worldwide in which a number of modern and sophisticated techniques and tools have been developed and employed. Many countries have invested in plant genome sequencing as part of a sustainable development strategy. Each year, the number of plant genomes and transcriptomes sequenced has increased. The results obtained offer opportunities for fundamental and applied research, provide valuable data for identification of genes or molecular markers linked to traits that are important for selection, cultivation, and/or production. In Vietnam, partial or complete genome sequencing of crops has been recently conducted, primarily as part of international collaborative projects. The genus Panax L. (Araliaceae family) is comprised of several species of commercial value with narrow distributions such as P. bipinnatifidus Seem., P. stipuleanatus H.T.Tsai & K.M.Feng, and Panax vietnamensis Ha et Grushv. Despite their very important roles in traditional medicine, understanding of their genetic characteristics is still limited. Molecular studies on the genus have, so far, only evaluated limited markers for phylogenetic analysis. Therefore, genome sequencing of these important herbal plants is needed to understand their genetic characteristics, their evolutionary history and the genes and biochemical pathways contributing to medicinally important metabolites. This review summarizes all related genome sequencing technologies including the most recent advances in the last decade and their applications in genome and transcriptome sequencing of plants in general and in the genus Panax L. in particular.

scholarly journals Evolutionary history and palaeoecology of brown bear in North-East Siberia re-examined using ancient DNA and stable isotopes from skeletal remains

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Alba Rey-Iglesia ◽  
Ana García-Vázquez ◽  
Eve C. Treadaway ◽  
Johannes van der Plicht ◽  
Gennady F. Baryshnikov ◽  
...  
Keyword(s):  
Stable Isotopes ◽  
Ancient Dna ◽  
Evolutionary History ◽  
Brown Bear ◽  
Skeletal Remains ◽  
East Siberia ◽  
North East

Ancient DNA provides new insights into the origin of the Chinese domestic horse

2009 ◽  
Vol 36 (3) ◽  
pp. 835-842 ◽  
Author(s):  
Dawei Cai ◽  
Zhuowei Tang ◽  
Lu Han ◽  
Camilla F. Speller ◽  
Dongya Y. Yang ◽  
...  
Keyword(s):  
Ancient Dna ◽  
Domestic Horse

Anthropological Applications of Ancient DNA: Problems and Prospects

2006 ◽  
Vol 71 (2) ◽  
pp. 365-380 ◽  
Author(s):  
Connie J. Mulligan
Keyword(s):  
Ancient Dna ◽  
Archaeological Remains ◽  
Research Strategies ◽  
Exogenous Dna ◽  
Extensive Training ◽  
Excellent Preservation ◽  
Successful Analysis ◽  
Adna Analysis ◽  
Widespread Interest ◽  
Careful Design

The analysis of DNA extracted from archaeological specimens to address anthropological questions is becoming increasingly common. Despite widespread interest in ancient DNA (aDNA), the difficulties inherent in aDNA analysis are not generally appreciated by researchers outside of the field. The majority of samples subjected to aDNA analysis often fail to produce results, and successful analysis is typically limited to specimens that exhibit excellent preservation. Contamination of samples with exogenous DNA is an ongoing problem and requires careful design of research strategies to limit and identify all DNA contaminants. Overall, aDNA analysis is a highly specialized and technical field that requires extensive training and can be quite expensive. Thus, each aDNA study should be carefully planned with significant input from archaeologists, physical anthropologists, linguists, and related researchers and should focus on well-preserved samples that are likely to produce a clear answer to a question that is not amenable to nongenetic analysis. In this manuscript, I explain the problems and prospects of various anthropological applications of aDNA technology. I present a series of previously published studies, which are of general anthropological interest, to illustrate the strengths and weaknesses of aDNA methods in each case. I also provide a checklist of questions to evaluate the utility of archaeological remains for aDNA analysis and to provide guidelines when designing an aDNA study.

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 .

Global distribution of the earliest shelly metazoans

1984 ◽  
Vol 121 (3) ◽  
pp. 185-188 ◽  
Author(s):  
Jiang Zhiwen
Keyword(s):  
Evolutionary History ◽  
Developmental Stages ◽  
Evolutionary Process ◽  
Global Distribution ◽  
Biological Factors ◽  
Animal Kingdom ◽  
Quantum Leap ◽  
History Of ◽  
Logical Extension

abstractThe appearance of the first abundant skeletal organisms in the earliest Cambrian was a quantum leap in the evolutionary history of life. It provided the foundations of the animal kingdom from Cambrian times onwards. This paper demonstrates that this evolutionary process resulted from a combination of environmental and biological factors. The author maintains that the appearance of the oldest shelly fossils is a reasonable criterion for defining the Precambrian–Cambrian boundary. This arises not only from the viewpoint of taking the Cambrian Period as the first period in the Palaeozoic Era, but is also a logical extension of regarding the history of life as being divisible into a series of developmental stages.

scholarly journals Genomics innovation: transforming healthcare, business, and the global economy

Genome ◽  
2015 ◽  
Vol 58 (12) ◽  
pp. 511-517 ◽  
Author(s):  
Gerardo Jimenez-Sanchez
Keyword(s):  
Environmental Sustainability ◽  
Global Economy ◽  
Scientific Evidence ◽  
Economic Value ◽  
Genomic Medicine ◽  
Health Food ◽  
Emerging Nations ◽  
Sequencing Technologies ◽  
Effective Selection ◽  
Alternative Sources

The genomics revolution has generated an unprecedented number of assets to propel innovation. Initial availability of genomics-based applications show a significant potential to contribute addressing global challenges, such as human health, food security, alternative sources of energies, and environmental sustainability. In the last years, most developed and emerging nations have established bioeconomy agendas where genomics plays a major role to meet their local needs. Genomic medicine is one of the most visible areas where genomics innovation is likely to contribute to a more individualized, predictive, and preventive medical practice. Examples in agriculture, dairy and beef, fishery, aquaculture, and forests industries include the effective selection of genetic variants associated to traits of economic value. Some, in addition to producing more and better foods, already represent an important increase in revenues to their respective industries. It is reasonable to predict that genomics applications will lead to a paradigm shift in our ability to ease significant health, economic, and social burdens. However, to successfully benefit from genomics innovations, it is imperative to address a number of hurdles related to generating robust scientific evidence, developing lower-cost sequencing technologies, effective bioinformatics, as well as sensitive ethical, economical, environmental, legal, and social aspects associated with the development and use of genomics innovations.

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