scholarly journals Population history of Antarctic and common minke whales inferred from individual whole-genome sequences

2016 ◽  
Vol 33 (2) ◽  
pp. 645-652 ◽  
Author(s):  
Takushi Kishida
Keyword(s):  
Population History ◽  
Whole Genome ◽  
Genome Sequences ◽  
Minke Whales ◽  
History Of

scholarly journals Insights into human genetic variation and population history from 929 diverse genomes

2019 ◽  
Author(s):  
Anders Bergström ◽  
Shane A. McCarthy ◽  
Ruoyun Hui ◽  
Mohamed A. Almarri ◽  
Qasim Ayub ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Central Africa ◽  
Population History ◽  
Human Populations ◽  
Genome Sequences ◽  
High Coverage ◽  
Geographical Regions ◽  
History Of ◽  
Different Populations ◽  
Source Populations

AbstractGenome sequences from diverse human groups are needed to understand the structure of genetic variation in our species and the history of, and relationships between, different populations. We present 929 high-coverage genome sequences from 54 diverse human populations, 26 of which are physically phased using linked-read sequencing. Analyses of these genomes reveal an excess of previously undocumented private genetic variation in southern and central Africa and in Oceania and the Americas, but an absence of fixed, private variants between major geographical regions. We also find deep and gradual population separations within Africa, contrasting population size histories between hunter-gatherer and agriculturalist groups in the last 10,000 years, a potentially major population growth episode after the peopling of the Americas, and a contrast between single Neanderthal but multiple Denisovan source populations contributing to present-day human populations. We also demonstrate benefits to the study of population relationships of genome sequences over ascertained array genotypes. These genome sequences are freely available as a resource with no access or analysis restrictions.

scholarly journals Whole-genome sequencing analysis reveals the population history of Mus musculus in Madagascar

2021 ◽  
Author(s):  
Kazumichi Fujiwara ◽  
Marie C Ranorosoa ◽  
Satoshi D Ohdachi ◽  
Satoru Arai ◽  
Yuki Sakuma ◽  
...  
Keyword(s):  
House Mouse ◽  
Mus Musculus ◽  
Population History ◽  
House Mice ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Mouse Population ◽  
Wide Range ◽  
History Of ◽  
Ancient Hybridization

AbstractIn Madagascar, the house mouse (Mus musculus) is thought to have colonized along with humans and is now one of the most successfully colonized rodents on the island. In this study, we determined the whole-genome sequences of the Madagascar house mouse captured from the wild. We examined the evolutionary history of its population regarding the mitochondrial and autosomal genomes. We confirmed that in the mitochondrial genomes of Madagascar house mice, a monophyletic clade forms a basal origin within the species. An analysis of autosomal genomic sequences indicates that the Madagascar house mouse population is genetically a member of M. m. castaneus (CAS). It also contains genetic elements of M. m. domesticus (DOM) resulting from ancient hybridization. The signature of a strong population bottleneck 1000–3000 years ago was observed in the mitochondrial and autosomal genomic data. We also show that the divergence of the Madagascar population from the CAS population occurred approximately 50,000–99,000 years ago. Madagascar house mice show strong genetic affinity to many CAS samples across a wide range of Indian Ocean coastal regions. However, our results suggest that they would not have originated directly from the Indonesian islands, where Austronesian-speaking people in Madagascar originated. Because the ancient hybridization signature with DOM did not appear in the Indonesian and other CAS samples, we propose that Madagascar house mice were not directly brought by Austronesian-speaking people but came from somewhere around the Middle East or South Asia soon after the colonization of initial farmers.

scholarly journals Whole-genome data reveal the complex history of a diverse ecological community

2018 ◽  
Vol 115 (28) ◽  
pp. E6507-E6515 ◽  
Author(s):  
Lynsey Bunnefeld ◽  
Jack Hearn ◽  
Graham N. Stone ◽  
Konrad Lohse
Keyword(s):  
Wide Distribution ◽  
Population History ◽  
Whole Genome ◽  
Ecological Communities ◽  
Widespread Species ◽  
Ecological Fitting ◽  
Genome Data ◽  
Western Palearctic ◽  
History Of ◽  
Alternative Community

How widespread ecological communities assemble remains a key question in ecology. Trophic interactions between widespread species may reflect a shared population history or ecological fitting of local pools of species with very different population histories. Which scenario applies is central to the stability of trophic associations and the potential for coevolution between species. Here we show how alternative community assembly hypotheses can be discriminated using whole-genome data for component species and provide a likelihood framework that overcomes current limitations in formal comparison of multispecies histories. We illustrate our approach by inferring the assembly history of a Western Palearctic community of insect herbivores and parasitoid natural enemies, trophic groups that together comprise 50% of terrestrial species. We reject models of codispersal from a shared origin and of delayed enemy pursuit of their herbivore hosts, arguing against herbivore attainment of “enemy-free space.” The community-wide distribution of species expansion times is also incompatible with a random, neutral model of assembly. Instead, we reveal a complex assembly history of single- and multispecies range expansions through the Pleistocene from different directions and over a range of timescales. Our results suggest substantial turnover in species associations and argue against tight coevolution in this system. The approach we illustrate is widely applicable to natural communities of nonmodel species and makes it possible to reveal the historical backdrop against which natural selection acts.

scholarly journals An African origin for Mycobacterium bovis

2020 ◽  
Vol 2020 (1) ◽  
pp. 49-59 ◽  
Author(s):  
Chloé Loiseau ◽  
Fabrizio Menardo ◽  
Abraham Aseffa ◽  
Elena Hailu ◽  
Balako Gumi ◽  
...  
Keyword(s):  
Population Structure ◽  
West Africa ◽  
Mycobacterium Bovis ◽  
Evolutionary History ◽  
Whole Genome ◽  
Genome Sequences ◽  
The World ◽  
History Of ◽  
Global Population ◽  
Different Parts

Abstract Background and objectives Mycobacterium bovis and Mycobacterium caprae are two of the most important agents of tuberculosis in livestock and the most important causes of zoonotic tuberculosis in humans. However, little is known about the global population structure, phylogeography and evolutionary history of these pathogens. Methodology We compiled a global collection of 3364 whole-genome sequences from M.bovis and M.caprae originating from 35 countries and inferred their phylogenetic relationships, geographic origins and age. Results Our results resolved the phylogenetic relationship among the four previously defined clonal complexes of M.bovis, and another eight newly described here. Our phylogeographic analysis showed that M.bovis likely originated in East Africa. While some groups remained restricted to East and West Africa, others have subsequently dispersed to different parts of the world. Conclusions and implications Our results allow a better understanding of the global population structure of M.bovis and its evolutionary history. This knowledge can be used to define better molecular markers for epidemiological investigations of M.bovis in settings where whole-genome sequencing cannot easily be implemented. Lay summary During the last few years, analyses of large globally representative collections of whole-genome sequences (WGS) from the human-adapted Mycobacterium tuberculosis complex (MTBC) lineages have enhanced our understanding of the global population structure, phylogeography and evolutionary history of these pathogens. In contrast, little corresponding data exists for M. bovis, the most important agent of tuberculosis in livestock. Using whole-genome sequences of globally distributed M. bovis isolates, we inferred the genetic relationships among different M. bovis genotypes distributed around the world. The most likely origin of M. bovis is East Africa according to our inferences. While some M. bovis groups remained restricted to East and West Africa, others have subsequently dispersed to different parts of the world driven by cattle movements.

scholarly journals Whole Genome Sequencing for Studying Bacillus anthracis from an Outbreak in the Abruzzo Region of Italy

2020 ◽  
Vol 8 (1) ◽  
pp. 87
Author(s):  
Alexandra Chiaverini ◽  
Mostafa Y. Abdel-Glil ◽  
Jörg Linde ◽  
Domenico Galante ◽  
Valeria Rondinone ◽  
...  
Keyword(s):  
Bacillus Anthracis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Southern Italy ◽  
Previous History ◽  
Whole Genome ◽  
Genome Sequences ◽  
Abruzzo Region ◽  
History Of ◽  
Bacterium Bacillus

Anthrax is a serious infectious disease caused by the gram-positive and spore-forming bacterium Bacillus anthracis. In Italy, anthrax is an endemic disease with sporadic cases each year and few outbreaks, especially in Southern Italy. However, new foci have been discovered in zones without previous history of anthrax. During summer 2016, an outbreak of anthrax caused the death of four goats in the Abruzzo region, where the disease had not been reported before. In order to investigate the outbreak, we sequenced one strain and compared it to 19 Italian B. anthracis genomes. Furthermore, we downloaded 71 whole genome sequences representing the global distribution of canonical SNP lineages and used them to verify the phylogenetic positioning. To this end, we analyzed and compared the genome sequences using canonical SNPs and the whole genome SNP-based analysis. Our results demonstrate that the outbreak strain belonged to the Trans-Eurasian (TEA) group A.Br.011/009, which is the predominant clade in Central-Southern Italy. In conclusion, the high genomic relatedness of the Italian TEA strains suggests their evolution from a common ancestor, while the spread is supposedly driven by trade as well as human and transhumance activities. Here, we demonstrated the capabilities of whole genome sequencing (WGS), which can be used as a tool for outbreak analyses and surveillance activities.

scholarly journals Complete Genome Sequences of Four Staphylococcus aureus Sequence Type 398 Isolates from Four Goats with Osteomyelitis

2018 ◽  
Vol 7 (12) ◽  
Author(s):  
Mohamed A. Abouelkhair ◽  
Rebecca E. Rifkin ◽  
Remiqiusz M. Grzeskowiak ◽  
Alexandru S. Biris ◽  
David E. Anderson ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Orthopedic Surgery ◽  
Sequence Type ◽  
Whole Genome Sequence ◽  
Multiple Infections ◽  
Whole Genome ◽  
Genome Sequences ◽  
Prosthetic Device ◽  
Content Type ◽  
History Of

Staphylococcus aureus is the causative agent of multiple infections, including bacteremia, infective endocarditis, osteomyelitis, septic arthritis, and prosthetic device infections. We report here the first whole-genome sequence for four S. aureus sequence type 398 isolates from clinical cases of osteomyelitis in four goats with a history of orthopedic surgery.

scholarly journals Insights into human genetic variation and population history from 929 diverse genomes

Science ◽  
2020 ◽  
Vol 367 (6484) ◽  
pp. eaay5012 ◽  
Author(s):  
Anders Bergström ◽  
Shane A. McCarthy ◽  
Ruoyun Hui ◽  
Mohamed A. Almarri ◽  
Qasim Ayub ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Central Africa ◽  
Population History ◽  
Human Populations ◽  
Genome Sequences ◽  
High Coverage ◽  
Geographical Regions ◽  
History Of ◽  
Different Populations ◽  
Source Populations

Genome sequences from diverse human groups are needed to understand the structure of genetic variation in our species and the history of, and relationships between, different populations. We present 929 high-coverage genome sequences from 54 diverse human populations, 26 of which are physically phased using linked-read sequencing. Analyses of these genomes reveal an excess of previously undocumented common genetic variation private to southern Africa, central Africa, Oceania, and the Americas, but an absence of such variants fixed between major geographical regions. We also find deep and gradual population separations within Africa, contrasting population size histories between hunter-gatherer and agriculturalist groups in the past 10,000 years, and a contrast between single Neanderthal but multiple Denisovan source populations contributing to present-day human populations.

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