scholarly journals Evolutionary history and genetic diversity of apomictic allopolyploids in Hieracium s.str.: morphological versus genomic features

2020 ◽  
Vol 107 (1) ◽  
pp. 66-90 ◽  
Author(s):  
Jindřich Chrtek ◽  
Patrik Mráz ◽  
Alexander Belyayev ◽  
Ladislava Paštová ◽  
Viera Mrázová ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Evolutionary History ◽  
Genomic Features

scholarly journals Genetic Diversity of Rice stripe necrosis virus and New Insights into Evolution of the Genus Benyvirus

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 737
Author(s):  
Issiaka Bagayoko ◽  
Marcos Giovanni Celli ◽  
Gustavo Romay ◽  
Nils Poulicard ◽  
Agnès Pinel-Galzi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Sierra Leone ◽  
Evolutionary History ◽  
Molecular Diversity ◽  
Genomic Data ◽  
Gene Recombination ◽  
Necrosis Virus ◽  
History Of ◽  
Complex Evolutionary History

The rice stripe necrosis virus (RSNV) has been reported to infect rice in several countries in Africa and South America, but limited genomic data are currently publicly available. Here, eleven RSNV genomes were entirely sequenced, including the first corpus of RSNV genomes of African isolates. The genetic variability was differently distributed along the two genomic segments. The segment RNA1, within which clusters of polymorphisms were identified, showed a higher nucleotidic variability than did the beet necrotic yellow vein virus (BNYVV) RNA1 segment. The diversity patterns of both viruses were similar in the RNA2 segment, except for an in-frame insertion of 243 nucleotides located in the RSNV tgbp1 gene. Recombination events were detected into RNA1 and RNA2 segments, in particular in the two most divergent RSNV isolates from Colombia and Sierra Leone. In contrast to BNYVV, the RSNV molecular diversity had a geographical structure with two main RSNV lineages distributed in America and in Africa. Our data on the genetic diversity of RSNV revealed unexpected differences with BNYVV suggesting a complex evolutionary history of the genus Benyvirus.

scholarly journals Intelligent Characterization of Lentil Genetic Resources: Evolutionary History, Genetic Diversity of Germplasm, and the Need for Well‐Represented Collections

2021 ◽  
Vol 1 (5) ◽  
Author(s):  
Azalea Guerra‐García ◽  
Tania Gioia ◽  
Eric Wettberg ◽  
Giuseppina Logozzo ◽  
Roberto Papa ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Resources ◽  
Evolutionary History

scholarly journals Evolutionary history and genetic connectivity across highly fragmented populations of an endangered daisy

Heredity ◽  
2021 ◽  
Author(s):  
Yael S. Rodger ◽  
Alexandra Pavlova ◽  
Steve Sinclair ◽  
Melinda Pickup ◽  
Paul Sunnucks
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Evolutionary History ◽  
Livestock Grazing ◽  
Genetic Connectivity ◽  
Evolutionary Divergence ◽  
Common Component ◽  
A Genome ◽  
Eastern Australia

AbstractConservation management can be aided by knowledge of genetic diversity and evolutionary history, so that ecological and evolutionary processes can be preserved. The Button Wrinklewort daisy (Rutidosis leptorrhynchoides) was a common component of grassy ecosystems in south-eastern Australia. It is now endangered due to extensive habitat loss and the impacts of livestock grazing, and is currently restricted to a few small populations in two regions >500 km apart, one in Victoria, the other in the Australian Capital Territory and nearby New South Wales (ACT/NSW). Using a genome-wide SNP dataset, we assessed patterns of genetic structure and genetic differentiation of 12 natural diploid populations. We estimated intrapopulation genetic diversity to scope sources for genetic management. Bayesian clustering and principal coordinate analyses showed strong population genetic differentiation between the two regions, and substantial substructure within ACT/NSW. A coalescent tree-building approach implemented in SNAPP indicated evolutionary divergence between the two distant regions. Among the populations screened, the last two known remaining Victorian populations had the highest genetic diversity, despite having among the lowest recent census sizes. A maximum likelihood population tree method implemented in TreeMix suggested little or no recent gene flow except potentially between very close neighbours. Populations that were more genetically distinctive had lower genetic diversity, suggesting that drift in isolation is likely driving population differentiation though loss of diversity, hence re-establishing gene flow among them is desirable. These results provide background knowledge for evidence-based conservation and support genetic rescue within and between regions to elevate genetic diversity and alleviate inbreeding.

scholarly journals SARS-Like Coronaviruses in Horseshoe Bats (Rhinolophus spp.) in Russia, 2020

Viruses ◽  
2022 ◽  
Vol 14 (1) ◽  
pp. 113
Author(s):  
Sergey Alkhovsky ◽  
Sergey Lenshin ◽  
Alexey Romashin ◽  
Tatyana Vishnevskaya ◽  
Oleg Vyshemirsky ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Evolutionary History ◽  
Structural Proteins ◽  
Rt Pcr ◽  
Phylogenetic Lineage ◽  
History Of ◽  
Horseshoe Bats ◽  
Regions Of Russia ◽  
Nonstructural Genes

We found and genetically described two novel SARS-like coronaviruses in feces and oral swabs of the greater (R. ferrumequinum) and the lesser (R. hipposideros) horseshoe bats in southern regions of Russia. The viruses, named Khosta-1 and Khosta-2, together with related viruses from Bulgaria and Kenya, form a separate phylogenetic lineage. We found evidence of recombination events in the evolutionary history of Khosta-1, which involved the acquisition of the structural proteins S, E, and M, as well as the nonstructural genes ORF3, ORF6, ORF7a, and ORF7b, from a virus that is related to the Kenyan isolate BtKY72. The examination of bats by RT-PCR revealed that 62.5% of the greater horseshoe bats in one of the caves were positive for Khosta-1 virus, while its overall prevalence was 14%. The prevalence of Khosta-2 was 1.75%. Our results show that SARS-like coronaviruses circulate in horseshoe bats in the region, and we provide new data on their genetic diversity.

scholarly journals Box, stalked, and upside-down? Draft genomes from diverse jellyfish (Cnidaria, Acraspeda) lineages: Alatina alata (Cubozoa), Calvadosia cruxmelitensis (Staurozoa), and Cassiopea xamachana (Scyphozoa)

GigaScience ◽  
2019 ◽  
Vol 8 (7) ◽  
Author(s):  
Aki Ohdera ◽  
Cheryl L Ames ◽  
Rebecca B Dikow ◽  
Ehsan Kayal ◽  
Marta Chiodin ◽  
...  
Keyword(s):  
Life History ◽  
Evolutionary History ◽  
Life History Traits ◽  
Hox Genes ◽  
Common Ancestor ◽  
Last Common Ancestor ◽  
Valuable Resource ◽  
Genomic Features ◽  
Cassiopea Xamachana ◽  
Nuisance Species

Abstract Background Anthozoa, Endocnidozoa, and Medusozoa are the 3 major clades of Cnidaria. Medusozoa is further divided into 4 clades, Hydrozoa, Staurozoa, Cubozoa, and Scyphozoa—the latter 3 lineages make up the clade Acraspeda. Acraspeda encompasses extraordinary diversity in terms of life history, numerous nuisance species, taxa with complex eyes rivaling other animals, and some of the most venomous organisms on the planet. Genomes have recently become available within Scyphozoa and Cubozoa, but there are currently no published genomes within Staurozoa and Cubozoa. Findings Here we present 3 new draft genomes of Calvadosia cruxmelitensis (Staurozoa), Alatina alata (Cubozoa), and Cassiopea xamachana (Scyphozoa) for which we provide a preliminary orthology analysis that includes an inventory of their respective venom-related genes. Additionally, we identify synteny between POU and Hox genes that had previously been reported in a hydrozoan, suggesting this linkage is highly conserved, possibly dating back to at least the last common ancestor of Medusozoa, yet likely independent of vertebrate POU-Hox linkages. Conclusions These draft genomes provide a valuable resource for studying the evolutionary history and biology of these extraordinary animals, and for identifying genomic features underlying venom, vision, and life history traits in Acraspeda.

Comparative mitochondrial phylogeography of two legless lizards (Pygopodidae) from Queensland’s fragmented woodlands

2020 ◽  
Vol 66 (3-4) ◽  
pp. 142-150
Author(s):  
Jessica Worthington Wilmer ◽  
Andrew P. Amey ◽  
Carmel McDougall ◽  
Melanie Venz ◽  
Stephen Peck ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Evolutionary History ◽  
The West ◽  
European Settlement ◽  
Low Genetic Diversity ◽  
Eastern Australia ◽  
Wide Range ◽  
History Of ◽  
Open Forests ◽  
Fossorial Species

Sclerophyll woodlands and open forests once covered vast areas of eastern Australia, but have been greatly fragmented and reduced in extent since European settlement. The biogeographic and evolutionary history of the biota of eastern Australia’s woodlands also remains poorly known, especially when compared to rainforests to the east, or the arid biome to the west. Here we present an analysis of patterns of mitochondrial genetic diversity in two species of Pygopodid geckos with distributions centred on the Brigalow Belt Bioregion of eastern Queensland. One moderately large and semi-arboreal species, Paradelma orientalis, shows low genetic diversity and no clear geographic structuring across its wide range. In contrast a small and semi-fossorial species, Delma torquata, consists of two moderately divergent clades, one from the ranges and upland of coastal areas of south-east Queensland, and other centred in upland areas further inland. These data point to varying histories of geneflow and refugial persistance in eastern Australia’s vast but now fragmented open woodlands. The Carnarvon Ranges of central Queensland are also highlighted as a zone of persistence for cool and/or wet-adapted taxa, however the evolutionary history and divergence of most outlying populations in these mountains remains unstudied.

scholarly journals Genome-Scale Phylogeny and Evolutionary Analysis of Ross River Virus Reveals Periodic Sweeps of Lineage Dominance in Western Australia, 1977–2014

2019 ◽  
Vol 94 (2) ◽  
Author(s):  
Alice Michie ◽  
Vijaykrishna Dhanasekaran ◽  
Michael D. A. Lindsay ◽  
Peter J. Neville ◽  
Jay Nicholson ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Western Australia ◽  
Evolutionary History ◽  
Gene Analysis ◽  
Ross River Virus ◽  
Whole Genome ◽  
Evolutionary Analysis ◽  
Genotype 4 ◽  
E2 Gene ◽  
Genome Scale

ABSTRACT Ross River virus (RRV), an alphavirus of the Togaviridae family, is the most medically significant mosquito-borne virus of Australia. Past RRV phylogenetic and evolutionary analyses have been based on partial genome analyses only. Three geographically distinct RRV lineages, the Eastern, the Western, and the supposedly extinct North-Eastern lineage, were classified previously. We sought to expand on past phylogenies through robust genome-scale phylogeny to better understand RRV genetic diversity and evolutionary dynamics. We analyzed 106 RRV complete coding sequences, which included 13 genomes available on NCBI and 94 novel sequences derived for this study, sampled throughout Western Australia (1977–2014) and during the substantial Pacific Islands RRV epidemic (1979–1980). Our final data set comprised isolates sampled over 59 years (1959–2018) from a range of locations. Four distinct genotypes were defined, with the newly described genotype 4 (G4) found to be the contemporary lineage circulating in Western Australia. The prior geographical classification of RRV lineages was not supported by our findings, with evidence of geographical and temporal cocirculation of distinct genetic groups. Bayesian Markov chain Monte Carlo (MCMC) analysis revealed that RRV lineages diverged from a common ancestor approximately 94 years ago, with distinct lineages emerging roughly every 10 years over the past 50 years in periodic bursts of genetic diversity. Our study has enabled a more robust analysis of RRV evolutionary history and resolved greater genetic diversity that had been previously defined by partial E2 gene analysis. IMPORTANCE Ross River virus (RRV) causes the most common mosquito-borne infection in Australia and causes a significant burden of suffering to infected individuals as well as being a large burden to the Australian economy. The genetic diversity of RRV and its evolutionary history have so far only been studied using partial E2 gene analysis with a limited number of isolates. Robust whole-genome analysis has not yet been conducted. This study generated 94 novel near-whole-genome sequences to investigate the evolutionary history of RRV to better understand its genetic diversity through comprehensive whole-genome phylogeny. A better understanding of RRV genetic diversity will enable better diagnostics, surveillance, and potential future vaccine design.

Genetic diversity, evolutionary history and implications for conservation of the lion (Panthera leo) in West and Central Africa

2011 ◽  
Vol 38 (7) ◽  
pp. 1356-1367 ◽  
Author(s):  
L. D. Bertola ◽  
W. F. van Hooft ◽  
K. Vrieling ◽  
D. R. Uit de Weerd ◽  
D. S. York ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Evolutionary History ◽  
Central Africa ◽  
Panthera Leo ◽  
West And Central Africa

scholarly journals How diverse can rare species be on the margins of genera distribution?

AoB Plants ◽  
2019 ◽  
Vol 11 (4) ◽  
Author(s):  
Alice Backes ◽  
Geraldo Mäder ◽  
Caroline Turchetto ◽  
Ana Lúcia Segatto ◽  
Jeferson N Fregonezi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Genetic Variability ◽  
Habitat Loss ◽  
Evolutionary History ◽  
Founder Effects ◽  
Geographical Isolation ◽  
Genetic Diversity And Structure ◽  
Genetic Patterns

Abstract Different genetic patterns have been demonstrated for narrowly distributed taxa, many of them linking rarity to evolutionary history. Quite a few species in young genera are endemics and have several populations that present low variability, sometimes attributed to geographical isolation or dispersion processes. Assessing the genetic diversity and structure of such species may be important for protecting them and understanding their diversification history. In this study, we used microsatellite markers and plastid sequences to characterize the levels of genetic variation and population structure of two endemic and restricted species that grow in isolated areas on the margin of the distribution of their respective genera. Plastid and nuclear diversities were very low and weakly structured in their populations. Evolutionary scenarios for both species are compatible with open-field expansions during the Pleistocene interglacial periods and genetic variability supports founder effects to explain diversification. At present, both species are suffering from habitat loss and changes in the environment can lead these species towards extinction.

scholarly journals Dog10K: an international sequencing effort to advance studies of canine domestication, phenotypes and health

2019 ◽  
Vol 6 (4) ◽  
pp. 810-824 ◽  
Author(s):  
Elaine A Ostrander ◽  
Guo-Dong Wang ◽  
Greger Larson ◽  
Bridgett M vonHoldt ◽  
Brian W Davis ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Architecture ◽  
Evolutionary History ◽  
De Novo ◽  
Mammalian Species ◽  
Aging Behavior ◽  
Extended Pedigrees ◽  
Geographical Variability ◽  
Whole Genomes

ABSTRACT Dogs are the most phenotypically diverse mammalian species, and they possess more known heritable disorders than any other non-human mammal. Efforts to catalog and characterize genetic variation across well-chosen populations of canines are necessary to advance our understanding of their evolutionary history and genetic architecture. To date, no organized effort has been undertaken to sequence the world's canid populations. The Dog10K Consortium (http://www.dog10kgenomes.org) is an international collaboration of researchers from across the globe who will generate 20× whole genomes from 10 000 canids in 5 years. This effort will capture the genetic diversity that underlies the phenotypic and geographical variability of modern canids worldwide. Breeds, village dogs, niche populations and extended pedigrees are currently being sequenced, and de novo assemblies of multiple canids are being constructed. This unprecedented dataset will address the genetic underpinnings of domestication, breed formation, aging, behavior and morphological variation. More generally, this effort will advance our understanding of human and canine health.

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