scholarly journals Contribution of historical herbarium small RNAs to the reconstruction of a cassava mosaic geminivirus evolutionary history

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Adrien Rieux ◽  
Paola Campos ◽  
Arnaud Duvermy ◽  
Sarah Scussel ◽  
Darren Martin ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Ecological Factors ◽  
Time Frame ◽  
African Cassava Mosaic Virus ◽  
Viral Diseases ◽  
Divergence Times ◽  
Herbarium Specimens ◽  
Small Interfering Rnas ◽  
Global Food Security ◽  
Technological Advances

AbstractEmerging viral diseases of plants are recognised as a growing threat to global food security. However, little is known about the evolutionary processes and ecological factors underlying the emergence and success of viruses that have caused past epidemics. With technological advances in the field of ancient genomics, it is now possible to sequence historical genomes to provide a better understanding of viral plant disease emergence and pathogen evolutionary history. In this context, herbarium specimens represent a valuable source of dated and preserved material. We report here the first historical genome of a crop pathogen DNA virus, a 90-year-old African cassava mosaic virus (ACMV), reconstructed from small RNA sequences bearing hallmarks of small interfering RNAs. Relative to tip-calibrated dating inferences using only modern data, those performed with the historical genome yielded both molecular evolution rate estimates that were significantly lower, and lineage divergence times that were significantly older. Crucially, divergence times estimated without the historical genome appeared in discordance with both historical disease reports and the existence of the historical genome itself. In conclusion, our study reports an updated time-frame for the history and evolution of ACMV and illustrates how the study of crop viral diseases could benefit from natural history collections.

The evolution of evolutionary ecology

2013 ◽  
Vol 59 (4) ◽  
pp. 172-180 ◽  
Author(s):  
Douglas J. Futuyma
Keyword(s):  
Climate Change ◽  
Life History ◽  
Community Ecology ◽  
Evolutionary History ◽  
Evolutionary Ecology ◽  
Natural World ◽  
Anthropogenic Climate Change ◽  
Future Evolution ◽  
Technological Advances ◽  
Evolution Of Life

Appreciation of ecology as a setting or stage for evolution has a long history, but evolutionary ecology became an identifiable discipline in the 1960's, growing mostly out of efforts to understand the evolution of life history components and to formulate a theory of community ecology based on the evolution of species' niches. Since the 1960's, technological advances and conceptual developments, especially the use of null hypotheses and an appreciation of the effects of evolutionary history and Earth history on current patterns, have altered and expanded evolutionary ecology. Many challenging questions remain poorly answered, especially the pressing question of how successful ongoing and future evolution will be in rescuing species from anthropogenic climate change and other human assaults on the natural world.

scholarly journals Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous–Paleogene boundary

2017 ◽  
Vol 114 (29) ◽  
pp. E5864-E5870 ◽  
Author(s):  
Yan-Jie Feng ◽  
David C. Blackburn ◽  
Dan Liang ◽  
David M. Hillis ◽  
David B. Wake ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Divergence Time ◽  
Divergence Times ◽  
Amphibian Species ◽  
Ancestral Area ◽  
Worldwide Distribution ◽  
Frog Species ◽  
Rapid Diversification ◽  
Molecular Dataset ◽  
Diverse Groups

Frogs (Anura) are one of the most diverse groups of vertebrates and comprise nearly 90% of living amphibian species. Their worldwide distribution and diverse biology make them well-suited for assessing fundamental questions in evolution, ecology, and conservation. However, despite their scientific importance, the evolutionary history and tempo of frog diversification remain poorly understood. By using a molecular dataset of unprecedented size, including 88-kb characters from 95 nuclear genes of 156 frog species, in conjunction with 20 fossil-based calibrations, our analyses result in the most strongly supported phylogeny of all major frog lineages and provide a timescale of frog evolution that suggests much younger divergence times than suggested by earlier studies. Unexpectedly, our divergence-time analyses show that three species-rich clades (Hyloidea, Microhylidae, and Natatanura), which together comprise ∼88% of extant anuran species, simultaneously underwent rapid diversification at the Cretaceous–Paleogene (K–Pg) boundary (KPB). Moreover, anuran families and subfamilies containing arboreal species originated near or after the KPB. These results suggest that the K–Pg mass extinction may have triggered explosive radiations of frogs by creating new ecological opportunities. This phylogeny also reveals relationships such as Microhylidae being sister to all other ranoid frogs and African continental lineages of Natatanura forming a clade that is sister to a clade of Eurasian, Indian, Melanesian, and Malagasy lineages. Biogeographical analyses suggest that the ancestral area of modern frogs was Africa, and their current distribution is largely associated with the breakup of Pangaea and subsequent Gondwanan fragmentation.

scholarly journals Tempo and mode of antibat ultrasound production and sonar jamming in the diverse hawkmoth radiation

2015 ◽  
Vol 112 (20) ◽  
pp. 6407-6412 ◽  
Author(s):  
Akito Y. Kawahara ◽  
Jesse R. Barber
Keyword(s):  
Evolutionary History ◽  
Tactile Stimulation ◽  
Phylogenetic Analyses ◽  
Physical Contact ◽  
Divergence Times ◽  
Entire Group ◽  
Multigene Phylogeny ◽  
Late Oligocene ◽  
Entire Family ◽  
Big Brown Bats

The bat–moth arms race has existed for over 60 million y, with moths evolving ultrasonically sensitive ears and ultrasound-producing organs to combat bat predation. The evolution of these defenses has never been thoroughly examined because of limitations in simultaneously conducting behavioral and phylogenetic analyses across an entire group. Hawkmoths include >1,500 species worldwide, some of which produce ultrasound using genital stridulatory structures. However, the function and evolution of this behavior remain largely unknown. We built a comprehensive behavioral dataset of hawkmoth hearing and ultrasonic reply to sonar attack using high-throughput field assays. Nearly half of the species tested (57 of 124 species) produced ultrasound to tactile stimulation or playback of bat echolocation attack. To test the function of ultrasound, we pitted big brown bats (Eptesicus fuscus) against hawkmoths over multiple nights and show that hawkmoths jam bat sonar. Ultrasound production was immediately and consistently effective at thwarting attack and bats regularly performed catching behavior without capturing moths. We also constructed a fossil-calibrated, multigene phylogeny to study the evolutionary history and divergence times of these antibat strategies across the entire family. We show that ultrasound production arose in multiple groups, starting in the late Oligocene (∼26 Ma) after the emergence of insectivorous bats. Sonar jamming and bat-detecting ears arose twice, independently, in the Miocene (18–14 Ma) either from earless hawkmoths that produced ultrasound in response to physical contact only, or from species that did not respond to touch or bat echolocation attack.

scholarly journals The diverging evolutionary history of opsin genes in Diptera

2020 ◽  
Author(s):  
Roberto Feuda ◽  
Matthew Goulty ◽  
Nicola Zadra ◽  
Tiziana Gasparetti ◽  
Ezio Rosato ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Turnover Rate ◽  
Selective Pressure ◽  
Ecological Factors ◽  
Peculiar Behaviour ◽  
Opsin Genes ◽  
History Of ◽  
Phylogenetic Framework ◽  
Independent Expansion ◽  
Dipteran Species

AbstractOpsin receptors mediate the visual process in animals and their evolutionary history can provide precious hints on the ecological factors that underpin their diversification. Here we mined the genomes of more than 60 Dipteran species and reconstructed the evolution of their opsin genes in a phylogenetic framework. Our phylogenies indicate that dipterans possess an ancestral set of five core opsins which have undergone several lineage-specific events including an independent expansion of low wavelength opsins in flies and mosquitoes and numerous family specific duplications and losses. Molecular evolutionary studies indicate that gene turnover rate, overall mutation rate, and site-specific selective pressure are higher in Anopheles than in Drosophila; we found signs of positive selection in both lineages, including events possibly associated with their peculiar behaviour. Our findings indicate an extremely variable pattern of opsin evolution in dipterans, showcasing how two similarly aged radiations - Anopheles and Drosophila - can be characterized by contrasting dynamics in the evolution of this gene family.

scholarly journals Geoarchaeological investigation of occupation deposits in Blombos Cave in South Africa indicate changes in site use and settlement dynamics in the southern Cape during MIS 5b-4

2020 ◽  
pp. 1-54
Author(s):  
Magnus M. Haaland ◽  
Christopher E. Miller ◽  
Ole F. Unhammer ◽  
Jerome P. Reynard ◽  
Karen L. van Niekerk ◽  
...  
Keyword(s):  
South Africa ◽  
Time Frame ◽  
Middle Stone Age ◽  
Sea Levels ◽  
Technological Advances ◽  
The Social ◽  
Settlement Dynamics ◽  
Site Use ◽  
Regional Settlement ◽  
Blombos Cave

Abstract The archaeological assemblage recovered from the Middle Stone Age (MSA) levels in Blombos Cave, South Africa, is central to our understanding of the development of early modern humans. Here, we demonstrate that the cultural and technological innovations inferred from the Blombos Cave MSA record also correlate with significant shifts in site use and occupational intensity. Through a comprehensive geoarchaeological investigation of three MSA occupation phases, we identified distinct diachronic trends in the frequency of visits and the modes of occupation. During the earliest phases (ca. 88–82 ka), humans inhabited the cave for more extended periods, but cave visits were not frequent. During the later phases (ca. 77–72 ka), the cave was more regularly visited but for shorter periods each time. We argue that these changes in local occupational intensity, which also coincide with shifts in vegetation, sea levels, and subsistence, can best be explained by broader changes in hunter-gatherer mobility strategies and occupation patterns. Fundamental changes in regional settlement dynamics during Marine Oxygen Isotope Stages 5b-4 would have significantly affected the nature and frequency of social interaction within and between prehistoric populations living in the southern Cape, a scenario that ultimately may explain some of the social and technological advances that occurred there during this time frame.

scholarly journals Permanent residents or temporary lodgers: characterizing intracellular bacterial communities in the siphonous green alga Bryopsis

2013 ◽  
Vol 280 (1754) ◽  
pp. 20122659 ◽  
Author(s):  
Joke Hollants ◽  
Frederik Leliaert ◽  
Heroen Verbruggen ◽  
Anne Willems ◽  
Olivier De Clerck
Keyword(s):  
Bacterial Communities ◽  
Evolutionary History ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Variation Partitioning ◽  
Bacterial Species ◽  
Bacterial Flora ◽  
Ecological Factors ◽  
Species Variation ◽  
Strong Impact ◽  
Intracellular Bacterial Communities

The ecological success of giant celled, siphonous green algae in coastal habitats has repeatedly been linked to endophytic bacteria living within the cytoplasm of the hosts. Yet, very little is known about the relative importance of evolutionary and ecological factors controlling the intracellular bacterial flora of these seaweeds. Using the marine alga Bryopsis (Bryopsidales, Chlorophyta) as a model, we explore the diversity of the intracellular bacterial communities and investigate whether their composition is controlled by ecological and biogeographic factors rather than the evolutionary history of the host. Using a combination of 16S rDNA clone libraries and denaturing gradient gel electrophoresis analyses, we show that Bryopsis harbours a mixture of relatively few but phylogenetically diverse bacterial species. Variation partitioning analyses show a strong impact of local environmental factors on the presence of Rickettsia and Mycoplasma in their association with Bryopsis . The presence of Flavobacteriaceae and Bacteroidetes, on the other hand, reflects a predominant imprint of host evolutionary history, suggesting that these bacteria are more specialized in their association. The results highlight the importance of interpreting the presence of individual bacterial phylotypes in the light of ecological and evolutionary principles such as phylogenetic niche conservatism to understand complex endobiotic communities and the parameters shaping them.

scholarly journals Diversity trends and their ontogenetic basis: an exploration of allometric disparity in rodents

2009 ◽  
Vol 277 (1685) ◽  
pp. 1227-1234 ◽  
Author(s):  
Laura A. B. Wilson ◽  
Marcelo R. Sánchez-Villagra
Keyword(s):  
Evolutionary History ◽  
Morphological Evolution ◽  
Ecological Factors ◽  
Morphological Diversity ◽  
Taxonomic Diversity ◽  
Morphological Integration ◽  
Morphological Features ◽  
Phylogenetic Relations ◽  
Ontogenetic Trajectories ◽  
Efficient Processing

It has been hypothesized that most morphological evolution occurs by allometric differentiation. Because rodents encapsulate a phenomenal amount of taxonomic diversity and, among several clades, contrasting levels of morphological diversity, they represent an excellent subject to address the question: how variable are allometric patterns during evolution? We investigated the influence of phylogenetic relations and ecological factors on the results of the first quantification of allometric disparity among rodents by exploring allometric space, a multivariate morphospace here derived from, and encapsulating all, the ontogenetic trajectories of 34 rodent species from two parallel phylogenetic radiations. Disparity was quantified using angles between ontogenetic trajectories for different species and clades. We found an overlapping occupation of allometric space by muroid and hystricognath species, revealing both clades possess similar abilities to evolve in different directions of phenotypic space, and anatomical diversity does not act to constrain the labile nature of allometric patterning. Morphological features to enable efficient processing of food serve to group rodents in allometric space, reflecting the importance of convergent morphology, rather than shared evolutionary history, in the generation of allometric patterns. Our results indicate that the conserved level of morphological integration found among primates cannot simply be extended to all mammals.

scholarly journals CRISPR-Based Genome Editing Tools: Insights into Technological Breakthroughs and Future Challenges

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 797
Author(s):  
Muntazir Mushtaq ◽  
Aejaz Ahmad Dar ◽  
Milan Skalicky ◽  
Anshika Tyagi ◽  
Nancy Bhagat ◽  
...  
Keyword(s):  
Genome Editing ◽  
Crop Improvement ◽  
Fine Tuning ◽  
Plant Genome ◽  
Base Editing ◽  
Global Food Security ◽  
Technological Advances ◽  
Efficient Delivery ◽  
Future Challenges ◽  
Recent Developments

Genome-editing (GE) is having a tremendous influence around the globe in the life science community. Among its versatile uses, the desired modifications of genes, and more importantly the transgene (DNA)-free approach to develop genetically modified organism (GMO), are of special interest. The recent and rapid developments in genome-editing technology have given rise to hopes to achieve global food security in a sustainable manner. We here discuss recent developments in CRISPR-based genome-editing tools for crop improvement concerning adaptation, opportunities, and challenges. Some of the notable advances highlighted here include the development of transgene (DNA)-free genome plants, the availability of compatible nucleases, and the development of safe and effective CRISPR delivery vehicles for plant genome editing, multi-gene targeting and complex genome editing, base editing and prime editing to achieve more complex genetic engineering. Additionally, new avenues that facilitate fine-tuning plant gene regulation have also been addressed. In spite of the tremendous potential of CRISPR and other gene editing tools, major challenges remain. Some of the challenges are related to the practical advances required for the efficient delivery of CRISPR reagents and for precision genome editing, while others come from government policies and public acceptance. This review will therefore be helpful to gain insights into technological advances, its applications, and future challenges for crop improvement.

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