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 A phylum-wide survey reveals multiple independent gains of head regeneration in Nemertea

2019 ◽  
Vol 286 (1898) ◽  
pp. 20182524 ◽  
Author(s):  
Eduardo E. Zattara ◽  
Fernando A. Fernández-Álvarez ◽  
Terra C. Hiebert ◽  
Alexandra E. Bely ◽  
Jon L. Norenburg
Keyword(s):  
Evolutionary History ◽  
Sequence Data ◽  
Ability To Regenerate ◽  
History Of ◽  
Phylogenetic Framework ◽  
Regenerative Ability ◽  
Head Regeneration

Animals vary widely in their ability to regenerate, suggesting that regenerative ability has a rich evolutionary history. However, our understanding of this history remains limited because regenerative ability has only been evaluated in a tiny fraction of species. Available comparative regeneration studies have identified losses of regenerative ability, yet clear documentation of gains is lacking. We assessed ability to regenerate heads and tails either through our own experiments or from literature reports for 35 species of Nemertea spanning the diversity of the phylum, including representatives of 10 families and all three orders. We generated a phylogenetic framework using sequence data to reconstruct the evolutionary history of head and tail regenerative ability across the phylum and found that all evaluated species can remake a posterior end but surprisingly few could regenerate a complete head. Our analysis reconstructs a nemertean ancestor unable to regenerate a head and indicates independent gains of head regenerative ability in at least four separate lineages, with one of these gains taking place as recently as the last 10–15 Myr. Our study highlights nemerteans as a valuable group for studying evolution of regeneration and identifying mechanisms associated with repeated gains of regenerative ability.

Evolution of physiological dormancy multiple times in Melastomataceae from Neotropical montane vegetation

2011 ◽  
Vol 22 (1) ◽  
pp. 37-44 ◽  
Author(s):  
Fernando A.O. Silveira ◽  
Rafaella C. Ribeiro ◽  
Denise M.T. Oliveira ◽  
G. Wilson Fernandes ◽  
José P. Lemos-Filho
Keyword(s):  
Phylogenetic Tree ◽  
Seed Dormancy ◽  
Rainy Season ◽  
Evolutionary History ◽  
Selective Pressure ◽  
Strong Selective Pressure ◽  
Montane Vegetation ◽  
Physiological Dormancy ◽  
History Of ◽  
Seed Coats

AbstractWe investigated seed dormancy among species of Melastomataceae from Neotropical montane vegetation of Brazil. Four out of 50 studied species had dormant seeds:Miconia corallina(Miconieae), Tibouchina cardinalis(Melastomeae), Comolia sertularia(Melastomeae) andChaetostoma armatum(Microlicieae). For these four species, germinability of seeds collected in different years was always < 10% and the percentages of embryoless seeds and non-viable embryos were both insufficient to explain low or null germinability. This is the first unequivocal report of seed dormancy in tropical Melastomataceae. The production of seeds with permeable seed coats and fully developed, differentiated embryos indicates the occurrence of physiological dormancy. The reconstructed phylogenetic tree of the 50 species suggests that physiological dormancy evolved multiple times during the evolutionary history of Melastomataceae in this vegetation. Physiological dormancy evolved in species and populations associated with xeric microhabitats, where seeds are dispersed in unfavourable conditions for establishment. Therefore, drought-induced mortality may have been a strong selective pressure favouring the evolution of physiological dormancy in Melastomataceae. We argue that dormancy may have been independently selected in other lineages of Cerrado plants colonizing xeric microhabitats and dispersing seeds at the end of the rainy season. The contributions of our data to the understanding of seed dormancy in tropical montane vegetation are discussed.

scholarly journals Migration without interbreeding: evolutionary history of a highly selfing Mediterranean grass inferred from whole genomes

2020 ◽  
Author(s):  
Christoph Stritt ◽  
Elena L. Gimmi ◽  
Michele Wyler ◽  
Abdelmonaim H. Bakali ◽  
Aleksandra Skalska ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Brachypodium Distachyon ◽  
Genotypic Diversity ◽  
Plant Evolution ◽  
Whole Genome ◽  
Continental Scale ◽  
Whole Genomes ◽  
History Of ◽  
Adaptive Phenotypic Plasticity ◽  
Independent Expansion

AbstractWhole genome sequences and coalescence theory allow the study of plant evolution in unprecedented detail. In this study we extend the genomic resources for the wild Mediterranean grass Brachypodium distachyon to investigate the scale of population structure and its underlying history at whole-genome resolution. The analysis of 196 accessions, spanning the Mediterranean from Iberia to Iraq, shows that the interplay of high selfing and seed dispersal rates has shaped genetic structure. At the continental scale, evolution in B. distachyon is characterized by the independent expansion of three lineages during the Upper Pleistocene. Today, these lineages may occur in sympatry yet do not interbreed. At the local scale, dispersal and selfing interact to maintain high genotypic diversity. Our study lays a foundation for the study of microevolution in B. distachyon and identifies adaptive phenotypic plasticity and frequency-dependent selection as key themes to be addressed with this model system.

scholarly journals Portiera gives new clues on the evolutionary history of whiteflies

2020 ◽  
Author(s):  
D. Santos-Garcia ◽  
N. Mestre-Rincon ◽  
D. Ouvrard ◽  
E. Zchori-Fein ◽  
S. Morin
Keyword(s):  
Evolutionary History ◽  
Target Genes ◽  
Common Ancestor ◽  
Genome Instability ◽  
Phylogenetic Reconstructions ◽  
Stability And Instability ◽  
History Of ◽  
Phylogenetic Framework ◽  
Phloem Feeding ◽  
Signal Saturation

AbstractWhiteflies (Hemiptera: Sternorrhyncha: Aleyrodidae) are a superfamily of small phloem-feeding insects. Their taxonomy is currently based on the morphology of nymphal stages that display phenotypic plasticity, which produces inconsistencies. To overcome this limitation, we developed a new phylogenetic framework that targets five genes of Candidatus Portiera aleyrodidarum, the primary endosymbiont of whiteflies. Portiera lineages have been co-diverging with whiteflies since their origin and therefore reflect their host evolutionary history. We also studied the origin of stability and instability in Portiera genomes by testing for the presence of two alternative gene rearrangements and the loss of a functional polymerase proofreading subunit (dnaQ), previously associated with genome instability. We present two phylogenetic reconstructions. One using the sequences of all five target genes from 22 whitefly species belonging to 17 genera. The second uses only two genes to include additional published Portiera sequences of 21 whitefly species, increasing our sampling size to 42 species from 25 genera. The developed framework showed low signal saturation, specificity to whitefly samples, and efficiency in solving inter-genera relationships and standing inconsistencies in the current taxonomy of the superfamily. Genome instability was found to be present only in the Aleurolobini tribe containing the Singhiella, Aleurolobus and Bemisia genera. This suggests that Portiera genome instability likely arose in the Aleurolobini tribe’s common ancestor, around 70 Mya. We propose a link between the switch from multi-bacteriocyte to a single-bacteriocyte mode of inheritance in the Aleurolobini tribe and the appearance of genome instability in Portiera.

scholarly journals Molecular palaeontology illuminates the evolution of ecdysozoan vision

2018 ◽  
Vol 285 (1892) ◽  
pp. 20182180 ◽  
Author(s):  
James F. Fleming ◽  
Reinhardt Møbjerg Kristensen ◽  
Martin Vinther Sørensen ◽  
Tae-Yoon S. Park ◽  
Kazuharu Arakawa ◽  
...  
Keyword(s):  
Colour Vision ◽  
Evolutionary History ◽  
Large Scale ◽  
Molecular Level ◽  
Visual Pigments ◽  
Gene Duplications ◽  
Opsin Genes ◽  
Integrative Study ◽  
Velvet Worms ◽  
History Of

Colour vision is known to have arisen only twice—once in Vertebrata and once within the Ecdysozoa, in Arthropoda. However, the evolutionary history of ecdysozoan vision is unclear. At the molecular level, visual pigments, composed of a chromophore and a protein belonging to the opsin family, have different spectral sensitivities and these mediate colour vision. At the morphological level, ecdysozoan vision is conveyed by eyes of variable levels of complexity; from the simple ocelli observed in the velvet worms (phylum Onychophora) to the marvellously complex eyes of insects, spiders, and crustaceans. Here, we explore the evolution of ecdysozoan vision at both the molecular and morphological level; combining analysis of a large-scale opsin dataset that includes previously unknown ecdysozoan opsins with morphological analyses of key Cambrian fossils with preserved eye structures. We found that while several non-arthropod ecdysozoan lineages have multiple opsins, arthropod multi-opsin vision evolved through a series of gene duplications that were fixed in a period of 35–71 million years (Ma) along the stem arthropod lineage. Our integrative study of the fossil and molecular record of vision indicates that fossils with more complex eyes were likely to have possessed a larger complement of opsin genes.

scholarly journals A phylum-wide survey reveals multiple independent gains of head regeneration ability in Nemertea

2018 ◽  
Author(s):  
Eduardo E. Zattara ◽  
Fernando A. Fernández-Álvarez ◽  
Terra C. Hiebert ◽  
Alexandra E. Bely ◽  
Jon L. Norenburg
Keyword(s):  
Evolutionary History ◽  
Sequence Data ◽  
Regeneration Ability ◽  
Tail Regeneration ◽  
Diverse Families ◽  
Ability To Regenerate ◽  
History Of ◽  
Phylogenetic Framework ◽  
Regenerative Ability ◽  
Head Regeneration

AbstractAnimals vary widely in their ability to regenerate, suggesting that regenerative abilities have a rich evolutionary history. However, our understanding of this history remains limited because regeneration ability has only been evaluated in a tiny fraction of species. Available comparative regeneration studies have identified losses of regenerative ability, yet clear documentation of gains is lacking. We surveyed regenerative ability in 34 species spanning the phylum Nemertea, assessing the ability to regenerate heads and tails either through our own experiments or from literature reports. Our sampling included representatives of the 10 most diverse families and all three orders comprising this phylum. We generated a phylogenetic framework using sequence data to reconstruct the evolutionary history of head and tail regeneration ability across the phylum and found that while all evaluated species can remake a posterior end, surprisingly few could regenerate a complete head. Our analysis reconstructs a nemertean ancestor unable to regenerate a head and indicates at least four separate lineages have independently gained head regeneration ability, one such gains reconstructed as taking place within the last 10-15 mya. Our study highlights nemerteans as a valuable group for studying evolution of regeneration and identifying mechanisms associated with repeated gains of regenerative ability.

Polyploidy and possible implications for the evolutionary history of some Australian Danthonieae

2010 ◽  
Vol 58 (1) ◽  
pp. 23 ◽  
Author(s):  
C. Waters ◽  
B. G. Murray ◽  
G. Melville ◽  
D. Coates ◽  
A. Young ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Potential Role ◽  
New South ◽  
Ecological Factors ◽  
Distribution Patterns ◽  
Low Frequencies ◽  
Rapid Speciation ◽  
South Wales ◽  
History Of

Polyploidy is a widespread feature of some plants that allows for rapid speciation and occurs widely in Poaceae. However, there have been few studies of Australian native grasses reporting the distribution patterns of cytotypes and examining the potential role of different cytotypes in adaptation. We determined chromosome number for 48, 113, 8, 43 and 33 plants of Austrodanthonia bipartita (Link) H.P.Linder, A. caespitosa (Gaudich.) H.P.Linder, A. eriantha (Lindl.) H.P.Linder, A. fulva (Vickery) H.P.Linder and A. setacea (R.Br.) H.P.Linder, respectively, representing 28 wild populations collected in central western New South Wales. A widespread distribution is reported for tetraploids (2n = 48), whereas diploids (2n = 24) and a limited number of hexaploids (2n = 72) appear to be associated with northern and western populations. In all populations, coexistent cytotypes were found, although tetraploids were the most widespread cytotype for the most commonly occurring species, A. caespitosa. The occurrence of low frequencies of putative intermediate cytotypes, particularly triploids, in all five species provides evidence for inter-specific hybridisation and/or intra-specific crossing between cytotypes. The lack of common ecological factors (climate, edaphic or micro-site) that clearly distinguish diploid from tetraploid A. caespitosa plants provides further evidence for hybridisation between cytological races of this species.

scholarly journals Tracing the History of LINE and SINE Extinction in Sigmodontine Rodents

2018 ◽  
Author(s):  
Lei Yang ◽  
Holly A Wichman
Keyword(s):  
Evolutionary History ◽  
Selective Pressure ◽  
Mammalian Genome ◽  
Group Activity ◽  
South American ◽  
Long Period ◽  
Strong Selective Pressure ◽  
Basal Group ◽  
History Of ◽  
Entire History

AbstractBackgroundL1 retrotransposons have co-evolved with their mammalian hosts for the entire history of mammals and currently make up to 20% of a typical mammalian genome. B1 retrotransposons are dependent on L1 for retrotransposition and span the evolutionary history of rodents since their radiation. L1s were found to have lost their activity in a group of South American rodents, the Sigmodontinae, and B1 inactivation preceded the extinction of L1 in the same group. Consequently, a basal group of sigmodontines have active L1s but inactive B1s and a derived clade have both inactive L1s and B1s. It has been suggested that B1s became extinct during a long period of L1 quiescence and that L1s subsequently reemerged in the basal group.ResultsHere we investigate the evolutionary histories of L1 and B1 in the sigmodontine rodents and show that L1 activity continued until after the split of the L1-extinct clade and the basal group. After the split, L1s had a small burst of activity in the former group, followed by extinction. In the basal group, activity was initially low but was followed by a dramatic increase in L1 activity. We found the last wave of B1s retrotransposition was large and probably preceded the split between the two rodent clades.ConclusionsGiven that L1s had been steadily retrotransposing during the time corresponding to B1 extinction and that the burst of B1 activity preceding B1 extinction was large, we conclude that B1 extinction was not a result of L1 quiescence. Rather, the burst of B1 activity may have contributed to L1 extinction both by competition with L1 and by putting strong selective pressure on the host to control retrotransposition.

scholarly journals A quantitative model for characterizing the evolutionary history of mammalian gene expression

2017 ◽  
Author(s):  
Jenny Chen ◽  
Ross Swofford ◽  
Jeremy Johnson ◽  
Beryl B. Cummings ◽  
Noga Rogel ◽  
...  
Keyword(s):  
Gene Expression ◽  
Evolutionary History ◽  
Selective Pressure ◽  
Mammalian Species ◽  
Quantitative Model ◽  
Process Models ◽  
Stabilizing Selection ◽  
Expression Data ◽  
Evolutionary Forces ◽  
History Of

AbstractCharacterizing the evolutionary history of a gene’s expression profile is a critical component for understanding the relationship between genotype, expression, and phenotype. However, it is not well-established how best to distinguish the different evolutionary forces acting on gene expression. Here, we use RNA-seq across 7 tissues from 17 mammalian species to show that expression evolution across mammals is accurately modeled by the Ornstein-Uhlenbeck (OU) process. This stochastic process models expression trajectories across time as Gaussian distributions whose variance is parameterized by the rate of genetic drift and strength of stabilizing selection. We use these mathematical properties to identify expression pathways under neutral, stabilizing, and directional selection, and quantify the extent of selective pressure on a gene’s expression. We further detect deleterious expression levels outside expected evolutionary distributions in expression data from individual patients. Our work provides a statistical framework for interpreting expression data across species and in disease.One Sentence SummaryWe demonstrate the power of a stochastic model for quantifying selective pressure on expression and estimating evolutionary distributions of optimal gene expression.

Why did some ichthyosaurs have such large eyes?

2002 ◽  
Vol 205 (4) ◽  
pp. 439-441
Author(s):  
Stuart Humphries ◽  
Graeme D. Ruxton
Keyword(s):  
Marine Mammals ◽  
Evolutionary History ◽  
Ecological Factors ◽  
Great Depth ◽  
Low Light ◽  
Deep Diving ◽  
Eye Size ◽  
History Of ◽  
Simultaneous Selection ◽  
Selection For

SUMMARY Many species of extinct marine ichthyosaurs had much larger eyes for their body size than would be expected of extant marine mammals and reptiles. Sensitivity to low light at great depth for the deep-diving genus Ophthalmosaurus has recently been suggested as the reason for the large eyes of these animals. Here, we discuss the implications for vision at such depths and consider other optical factors determining eye size. We suggest that the large eyes of ichthyosaurs are more likely to be the result of simultaneous selection for both sensitivity to low light and visual acuity. The importance of the evolutionary history of extant marine mammals and extinct ichthyosaurs is discussed, as are ecological factors driving both acuity and sensitivity.

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