scholarly journals The evolution of insect visual opsin genes with specific consideration of the influence of ocelli and life history traits

2022 ◽  
Vol 22 (1) ◽  
Author(s):  
Quentin Guignard ◽  
Jeremy D. Allison ◽  
Bernard Slippers
Keyword(s):  
Life History ◽  
Life History Traits ◽  
Sequence Data ◽  
Pcr Amplification ◽  
Compound Eyes ◽  
Phylogenetic Groups ◽  
Evolutionary Forces ◽  
Opsin Genes ◽  
Gains And Losses ◽  
Insight Into

Abstract Background Visual opsins are expressed in the compound eyes and ocelli of insects and enable light detection. Three distinct phylogenetic groups of visual opsins are found in insects, named long (LW), short (SW) and ultraviolet (UV) wavelength sensitive opsins. Recently, the LW group was found to be duplicated into the LW2b and the LW2a opsins. The expression of LW2b opsins is ocelli specific in some insects (e.g., bees, cricket, scorpion flies), but the gene was not found in other orders possessing three or less ocelli (e.g., dragonflies, beetles, moths, bugs). In flies, two LW2b homologs have been characterised, with one expressed in the ocelli and the other in the compound eyes. To date, it remains unclear which evolutionary forces have driven gains and losses of LW opsins in insects. Here we take advantage of the recent rapid increase in available sequence data (i.e., from insect genomes, targeted PCR amplification, RNAseq) to characterize the phylogenetic relationships of 1000 opsin sequences in 18 orders of Insects. The resulting phylogeny discriminates between four main groups of opsins, and onto this phylogeny we mapped relevant morphological and life history traits. Results Our results demonstrate a conserved LW2b opsin only present in insects with three ocelli. Only two groups (Brachycera and Odonata) possess more than one LW2b opsin, likely linked to their life history. In flies, we hypothesize that the duplication of the LW2b opsin occurred after the transition from aquatic to terrestrial larvae. During this transition, higher flies (Brachycera) lost a copy of the LW2a opsin, still expressed and duplicated in the compound eyes of lower flies (Nematocera). In higher flies, the LW2b opsin has been duplicated and expressed in the compound eyes while the ocelli and the LW2b opsin were lost in lower flies. In dragonflies, specialisation of flight capabilities likely drove the diversification of the LW2b visual opsins. Conclusion The presence of the LW2b opsin in insects possessing three ocelli suggests a role in specific flight capabilities (e.g., stationary flight). This study provides the most complete view of the evolution of visual opsin genes in insects yet, and provides new insight into the influence of ocelli and life history traits on opsin evolution in insects.

scholarly journals The Evolution of Insect Visual Opsin Genes With Specific Consideration of the Influence of Ocelli and Life History Traits

2021 ◽  
Author(s):  
Quentin Guignard ◽  
Jeremy D. Allison ◽  
Bernard Slippers
Keyword(s):  
Life History ◽  
Life History Traits ◽  
Sequence Data ◽  
The Other ◽  
Compound Eyes ◽  
Phylogenetic Groups ◽  
Evolutionary Forces ◽  
Opsin Genes ◽  
Gains And Losses ◽  
Insight Into

Abstract Background: Visual opsins are expressed in the compound eyes and ocelli of insects and enable light detection. Three distinct phylogenetic groups of visual opsins are found in insects, named long (LW), short (SW) and ultraviolet (UV) wavelength sensitive opsins. Recently, the LW group was found to be duplicated into the ancestral LW2b and the more recent LW2a opsins. The expression of LW2b opsins is ocelli specific in some insects (e.g., bees, cricket, scorpion flies), but the gene was absent in other orders possessing three or less ocelli (e.g., dragonflies, beetles, moth, bugs). In flies, two LW2b homologs have been characterised, with one expressed in the ocelli and the other in the compound eyes. To date, it remains unclear which evolutionary forces have driven gains and losses of LW opsins in insects. Here we take advantage of the recent rapid increase in available sequence data from insect genomes to characterize the phylogenetic relationships of 1000 opsin sequences in 18 orders of Insects. The resulting phylogeny discriminates between four main groups of opsins, and onto this phylogeny we mapped relevant morphological and life history traits.Results: Our results demonstrate a conserved LW2b opsin only present in insects with three ocelli. Only two taxa (flies and dragonflies) possess more than one LW2b opsin, likely linked to their life history. In flies, we hypothesize that the duplication of the LW2b opsin occurred after the transition from aquatic to terrestrial larvae. During this transition, higher flies (Brachycera) lost a copy of the LW2a opsin, still expressed in the compound eyes of lower flies (Nematocera). In higher flies, the LW2b opsin has been duplicated and expressed in the compound eyes while the ocelli and the LW2b opsin were lost in lower flies. In dragonflies, specialisation of the visual system likely drove the diversification of visual opsins.Conclusion: The presence of the LW2b opsin in insects possessing three ocelli suggests a role in flight. This study provides the most complete view of the evolution of visual opsin genes in insects yet, and provides new insight into the influence of ocelli and life history traits on opsin evolution in insects.

scholarly journals Life-history traits and habitat availability shape genomic diversity in birds: implications for conservation

2021 ◽  
Vol 288 (1961) ◽  
Author(s):  
Anna Brüniche-Olsen ◽  
Kenneth F. Kellner ◽  
Jerrold L. Belant ◽  
J. Andrew DeWoody
Keyword(s):  
Life History ◽  
Life History Traits ◽  
Management Practices ◽  
Sequence Data ◽  
Extinction Risk ◽  
Conservation Status ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
Whole Genome Sequence ◽  
Habitat Availability

More than 25% of species assessed by the International Union for Conservation of Nature (IUCN) are threatened with extinction. Understanding how environmental and biological processes have shaped genomic diversity may inform management practices. Using 68 extant avian species, we parsed the effects of habitat availability and life-history traits on genomic diversity over time to provide a baseline for conservation efforts. We used published whole-genome sequence data to estimate overall genomic diversity as indicated by historical long-term effective population sizes ( N e ) and current genomic variability ( H ), then used environmental niche modelling to estimate Pleistocene habitat dynamics for each species. We found that N e and H were positively correlated with habitat availability and related to key life-history traits (body mass and diet), suggesting the latter contribute to the overall genomic variation. We found that H decreased with increasing species extinction risk, suggesting that H may serve as a leading indicator of demographic trends related to formal IUCN conservation status in birds. Our analyses illustrate that genome-wide summary statistics estimated from sequence data reflect meaningful ecological attributes relevant to species conservation.

scholarly journals Cnidarian Pattern Recognition Receptor Repertoires Reflect Both Phylogeny and Life History Traits

2021 ◽  
Vol 12 ◽  
Author(s):  
Madison A. Emery ◽  
Bradford A. Dimos ◽  
Laura D. Mydlarz
Keyword(s):  
Pattern Recognition ◽  
Innate Immunity ◽  
Life History ◽  
Life History Traits ◽  
Innate Immune ◽  
Immune Pathways ◽  
Immune Pathway ◽  
Molecular Patterns ◽  
Insight Into ◽  
Recognition Receptor

Pattern recognition receptors (PRRs) are evolutionarily ancient and crucial components of innate immunity, recognizing danger-associated molecular patterns (DAMPs) and activating host defenses. Basal non-bilaterian animals such as cnidarians must rely solely on innate immunity to defend themselves from pathogens. By investigating cnidarian PRR repertoires we can gain insight into the evolution of innate immunity in these basal animals. Here we utilize the increasing amount of available genomic resources within Cnidaria to survey the PRR repertoires and downstream immune pathway completeness within 15 cnidarian species spanning two major cnidarian clades, Anthozoa and Medusozoa. Overall, we find that anthozoans possess prototypical PRRs, while medusozoans appear to lack these immune proteins. Additionally, anthozoans consistently had higher numbers of PRRs across all four classes relative to medusozoans, a trend largely driven by expansions in NOD-like receptors and C-type lectins. Symbiotic, sessile, and colonial cnidarians also have expanded PRR repertoires relative to their non-symbiotic, mobile, and solitary counterparts. Interestingly, cnidarians seem to lack key components of mammalian innate immune pathways, though similar to PRR numbers, anthozoans possess more complete immune pathways than medusozoans. Together, our data indicate that anthozoans have greater immune specificity than medusozoans, which we hypothesize to be due to life history traits common within Anthozoa. Overall, this investigation reveals important insights into the evolution of innate immune proteins within these basal animals.

scholarly journals Inference of past demography, dormancy and self-fertilization rates from whole genome sequence data

2019 ◽  
Author(s):  
Thibaut Sellinger ◽  
Diala Abu Awad ◽  
Markus Möst ◽  
Aurélien Tellier
Keyword(s):  
Life History ◽  
Genome Sequence ◽  
Life History Traits ◽  
Sequence Data ◽  
Demographic History ◽  
Full Genome Sequence ◽  
Egg Bank ◽  
Genome Sequence Data ◽  
Self Fertilization ◽  
Population Demographic

AbstractSeveral methods based on the Sequential Markovian Coalescent (SMC) have been developed to use full genome sequence data to uncover population demographic history, which is of interest in its own right and a key requirement to generate a null model for selection tests. While these methods can be applied to all possible species, the underlying assumptions are sexual reproduction at each generation and no overlap of generations. However, in many plant, invertebrate, fungi and other species, those assumptions are often violated due to different ecological and life history traits, such as self-fertilization or long term dormant structures (seed or egg-banking). We develop a novel SMC-based method to infer 1) the rates of seed/egg-bank and of self-fertilization, and 2) the populations’ past demographic history. Using simulated data sets, we demonstrate the accuracy of our method for a wide range of demographic scenarios and for sequence lengths from one to 30 Mb using four sampled genomes. Finally, we apply our method to a Swedish and a German population of Arabidopsis thaliana demonstrating a selfing rate of ca. 0.8 and the absence of any detectable seed-bank. In contrast, we show that the water flea Daphnia pulex exhibits a long lived egg-bank of three to 18 generations. In conclusion, we here present a novel method to infer accurate demographies and life-history traits for species with selfing and/or seed/egg-banks. Finally, we provide recommendations on the use of SMC-based methods for non-model organisms, highlighting the importance of the per site and the effective ratios of recombination over mutation.

Prey tell: what quillback rockfish early life history traits reveal about their survival in encounters with juvenile coho salmon

2020 ◽  
Vol 650 ◽  
pp. 7-18 ◽  
Author(s):  
HW Fennie ◽  
S Sponaugle ◽  
EA Daly ◽  
RD Brodeur
Keyword(s):  
Life History ◽  
Early Life ◽  
Life History Traits ◽  
Direct Evidence ◽  
Coho Salmon ◽  
Larval Fish ◽  
Early Life History ◽  
In The Wild ◽  
Otolith Microstructure Analysis ◽  
Pelagic Juvenile

Predation is a major source of mortality in the early life stages of fishes and a driving force in shaping fish populations. Theoretical, modeling, and laboratory studies have generated hypotheses that larval fish size, age, growth rate, and development rate affect their susceptibility to predation. Empirical data on predator selection in the wild are challenging to obtain, and most selective mortality studies must repeatedly sample populations of survivors to indirectly examine survivorship. While valuable on a population scale, these approaches can obscure selection by particular predators. In May 2018, along the coast of Washington, USA, we simultaneously collected juvenile quillback rockfish Sebastes maliger from both the environment and the stomachs of juvenile coho salmon Oncorhynchus kisutch. We used otolith microstructure analysis to examine whether juvenile coho salmon were age-, size-, and/or growth-selective predators of juvenile quillback rockfish. Our results indicate that juvenile rockfish consumed by salmon were significantly smaller, slower growing at capture, and younger than surviving (unconsumed) juvenile rockfish, providing direct evidence that juvenile coho salmon are selective predators on juvenile quillback rockfish. These differences in early life history traits between consumed and surviving rockfish are related to timing of parturition and the environmental conditions larval rockfish experienced, suggesting that maternal effects may substantially influence survival at this stage. Our results demonstrate that variability in timing of parturition and sea surface temperature leads to tradeoffs in early life history traits between growth in the larval stage and survival when encountering predators in the pelagic juvenile stage.

Life History Traits in a Population of Pelobates syriacus (Boettger, 1889) from Turkey

2020 ◽  
Vol 27 (4) ◽  
pp. 195-200
Author(s):  
Ufuk Bülbül ◽  
Halime Koç ◽  
Yasemin Odabaş ◽  
Ali İhsan Eroğlu ◽  
Muammer Kurnaz ◽  
...  
Keyword(s):  
Life History ◽  
Age Structure ◽  
Life History Traits ◽  
Spadefoot Toad ◽  
Males And Females

Age structure of the eastern spadefoot toad, Pelobates syriacus from the Kızılırmak Delta (Turkey) were assessed using phalangeal skeletochronology. Snout-vent length (SVL) ranged from 42.05 to 86.63 mm in males and 34.03 to 53.27 mm in females. Age of adults ranged from 2 to 8 years in males and 3 to 5 years in females. For both sexes, SVL was significantly correlated with age. Males and females of the toads reached maturity at 2 years of age.

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