scholarly journals Genomic bases underlying the adaptive radiation of core landbirds

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yonghua Wu ◽  
Yi Yan ◽  
Yuanqin Zhao ◽  
Li Gu ◽  
Songbo Wang ◽  
...  
Keyword(s):  
Adaptive Radiation ◽  
Strong Support ◽  
Bright Light ◽  
Ecological Niches ◽  
Ecological Diversification ◽  
Fat Digestion ◽  
Genome Wide ◽  
Adaptive Enhancement ◽  
Dietary Niche ◽  
Dim Light

Abstract Background Core landbirds undergo adaptive radiation with different ecological niches, but the genomic bases that underlie their ecological diversification remain unclear. Results Here we used the genome-wide target enrichment sequencing of the genes related to vision, hearing, language, temperature sensation, beak shape, taste transduction, and carbohydrate, protein and fat digestion and absorption to examine the genomic bases underlying their ecological diversification. Our comparative molecular phyloecological analyses show that different core landbirds present adaptive enhancement in different aspects, and two general patterns emerge. First, all three raptorial birds (Accipitriformes, Strigiformes, and Falconiformes) show a convergent adaptive enhancement for fat digestion and absorption, while non-raptorial birds tend to exhibit a promoted capability for protein and carbohydrate digestion and absorption. Using this as a molecular marker, our results show relatively strong support for the raptorial lifestyle of the common ancestor of core landbirds, consequently suggesting a single origin of raptors, followed by two secondary losses of raptorial lifestyle within core landbirds. In addition to the dietary niche, we find at temporal niche that diurnal birds tend to exhibit an adaptive enhancement in bright-light vision, while nocturnal birds show an increased adaption in dim-light vision, in line with previous findings. Conclusions Our molecular phyloecological study reveals the genome-wide adaptive differentiations underlying the ecological diversification of core landbirds.

scholarly journals Genomic bases underlying the adaptive radiation of core landbirds

2020 ◽  
Author(s):  
Yonghua Wu ◽  
Yi Yan ◽  
Yuanqin Zhao ◽  
Li Gu ◽  
Songbo Wang ◽  
...  
Keyword(s):  
Adaptive Radiation ◽  
Strong Support ◽  
Bright Light ◽  
Ecological Niches ◽  
Ecological Diversification ◽  
Fat Digestion ◽  
Genome Wide ◽  
Adaptive Enhancement ◽  
Dietary Niche ◽  
Dim Light

AbstractCore landbirds undergo adaptive radiation with different ecological niches, but the genomic bases that underlie their ecological diversification remain unclear. Here we used the genome-wide target enrichment sequencing of the genes related to vision, hearing, language, temperature sensation, beak shape, taste transduction, and carbohydrate, protein and fat digestion and absorption to examine the genomic bases underlying their ecological diversification. Our comparative molecular phyloecological analyses show that different core landbirds present adaptive enhancement in different aspects, and two general patterns emerge. First, all three raptorial birds (Accipitriformes, Strigiformes, and Falconiformes) show a convergent adaptive enhancement for fat digestion and absorption, while non-raptorial birds tend to exhibit a promoted capability for protein and carbohydrate digestion and absorption. Using this as a molecular marker, our results show relatively strong support for the raptorial lifestyle of the common ancestor of core landbirds, consequently suggesting a single origin of raptors, followed by two secondary losses of raptorial lifestyle within core landbirds. In addition to the dietary niche, we find at temporal niche that diurnal birds tend to exhibit an adaptive enhancement in bright-light vision, while nocturnal birds show an increased adaption in dim-light vision, in line with previous findings. Our molecular phyloecological study reveals the genome-wide adaptive differentiations underlying the ecological diversification of core landbirds.

scholarly journals Evolutionary transformation of rod photoreceptors in the all-cone retina of a diurnal garter snake

2015 ◽  
Vol 113 (2) ◽  
pp. 356-361 ◽  
Author(s):  
Ryan K. Schott ◽  
Johannes Müller ◽  
Clement G. Y. Yang ◽  
Nihar Bhattacharyya ◽  
Natalie Chan ◽  
...  
Keyword(s):  
Strong Support ◽  
Bright Light ◽  
Cell Types ◽  
Garter Snake ◽  
Historical Contingency ◽  
Molecular Machinery ◽  
Dim Light ◽  
Cone Opsins ◽  
And Function ◽  
Evolutionary Fate

Vertebrate retinas are generally composed of rod (dim-light) and cone (bright-light) photoreceptors with distinct morphologies that evolved as adaptations to nocturnal/crepuscular and diurnal light environments. Over 70 years ago, the “transmutation” theory was proposed to explain some of the rare exceptions in which a photoreceptor type is missing, suggesting that photoreceptors could evolutionarily transition between cell types. Although studies have shown support for this theory in nocturnal geckos, the origins of all-cone retinas, such as those found in diurnal colubrid snakes, remain a mystery. Here we investigate the evolutionary fate of the rods in a diurnal garter snake and test two competing hypotheses: (i) that the rods, and their corresponding molecular machinery, were lost or (ii) that the rods were evolutionarily modified to resemble, and function, as cones. Using multiple approaches, we find evidence for a functional and unusually blue-shifted rhodopsin that is expressed in small single “cones.” Moreover, these cones express rod transducin and have rod ultrastructural features, providing strong support for the hypothesis that they are not true cones, as previously thought, but rather are modified rods. Several intriguing features of garter snake rhodopsin are suggestive of a more cone-like function. We propose that these cone-like rods may have evolved to regain spectral sensitivity and chromatic discrimination as a result of ancestral losses of middle-wavelength cone opsins in early snake evolution. This study illustrates how sensory evolution can be shaped not only by environmental constraints but also by historical contingency in forming new cell types with convergent functionality.

Bacterial origin of thymidylate and folate metabolism in Asgard Archaea

2021 ◽  
Author(s):  
Jonathan Filee ◽  
Hubert J. Becker ◽  
Lucille Mellottee ◽  
Zhihui LI ◽  
Jean-Christophe Lambry ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Lateral Gene Transfer ◽  
Phylogenetic Trees ◽  
De Novo ◽  
Horizontal Transmission ◽  
Folate Metabolism ◽  
Ecological Niches ◽  
Sequence Information ◽  
Amino Acid Utilization ◽  
Genome Wide

Little is known about the evolution and biosynthetic function of DNA precursor and the folate metabolism in the Asgard group of archaea. As Asgard occupy a key position in the archaeal and eukaryotic phylogenetic trees, we have exploited very recently emerged genome and metagenome sequence information to investigate these central metabolic pathways. Our genome-wide analyses revealed that the recently cultured Asgard archaeon Candidatus Prometheoarchaeum syntrophicum strain MK-D1 (Psyn) contains a complete folate-dependent network for the biosynthesis of DNA/RNA precursors, amino acids and syntrophic amino acid utilization. Altogether our experimental and computational data suggest that phylogenetic incongruences of functional folate-dependent enzymes from Asgard archaea reflect their persistent horizontal transmission from various bacterial groups, which has rewired the key metabolic reactions in an important and recently identified archaeal phylogenetic group. We also experimentally validated the functionality of the lateral gene transfer of Psyn thymidylate synthase ThyX. This enzyme uses bacterial-like folates efficiently and is inhibited by mycobacterial ThyX inhibitors. Our data raise the possibility that the thymidylate metabolism, required for de novo DNA synthesis, originated in bacteria and has been independently transferred to archaea and eukaryotes. In conclusion, our study has revealed that recent prevalent lateral gene transfer has markedly shaped the evolution of Asgard archaea by allowing them to adapt to specific ecological niches.

If You’re Happy and You Know it Stay Alert: The Effects of Lighting on Vigilance Performance and Affective State

2021 ◽  
Vol 65 (1) ◽  
pp. 854-858
Author(s):  
Lauren E. Monroe ◽  
Samantha L. Smith
Keyword(s):  
Affective State ◽  
Light Condition ◽  
Bright Light ◽  
Extended Period ◽  
Light Therapy ◽  
Speed Of Information Processing ◽  
Attention Tasks ◽  
High Workload ◽  
Dim Light ◽  
Over Time

Vigilance, or sustained attention tasks involve detecting critical signals, embedded amid more frequent neutral signals, over an extended period of time. A decline in performance, engagement, and arousal over time, as well as high workload and stress, are common outcomes of such tasks. Exposure to broad-spectrum or short wavelength bright light has been found to positively impact alertness, speed of information processing, and mood, but has not been extensively explored in the vigilance domain. The present study explored whether a light therapy lamp could mitigate the negative vigilance outcomes found in both performance and affective state. Results indicated that the therapy light did not prevent a decline in detection of critical signals over time, nor significantly impact workload, sleepiness, or subjective stress state compared to a dim light condition. However, mood questionnaire results suggest that lighting may impact separate constructs of arousal and tiredness, warranting further research.

scholarly journals Adaptation limits ecological diversification and promotes ecological tinkering during the competition for substitutable resources

2018 ◽  
Vol 115 (44) ◽  
pp. E10407-E10416 ◽  
Author(s):  
Benjamin H. Good ◽  
Stephen Martis ◽  
Oskar Hallatschek
Keyword(s):  
Evolutionary Dynamics ◽  
Competitive Exclusion ◽  
Directional Selection ◽  
Ecological Niches ◽  
Ecological Diversification ◽  
Effective Competition ◽  
Uptake Rates ◽  
Wide Range ◽  
Dynamical Features ◽  
Adaptation Limits

Microbial communities can evade competitive exclusion by diversifying into distinct ecological niches. This spontaneous diversification often occurs amid a backdrop of directional selection on other microbial traits, where competitive exclusion would normally apply. Yet despite their empirical relevance, little is known about how diversification and directional selection combine to determine the ecological and evolutionary dynamics within a community. To address this gap, we introduce a simple, empirically motivated model of eco-evolutionary feedback based on the competition for substitutable resources. Individuals acquire heritable mutations that alter resource uptake rates, either by shifting metabolic effort between resources or by increasing the overall growth rate. While these constitutively beneficial mutations are trivially favored to invade, we show that the accumulated fitness differences can dramatically influence the ecological structure and evolutionary dynamics that emerge within the community. Competition between ecological diversification and ongoing fitness evolution leads to a state of diversification–selection balance, in which the number of extant ecotypes can be pinned below the maximum capacity of the ecosystem, while the ecotype frequencies and genealogies are constantly in flux. Interestingly, we find that fitness differences generate emergent selection pressures to shift metabolic effort toward resources with lower effective competition, even in saturated ecosystems. We argue that similar dynamical features should emerge in a wide range of models with a mixture of directional and diversifying selection.

scholarly journals On the Diversification of the Translation Apparatus across Eukaryotes

2012 ◽  
Vol 2012 ◽  
pp. 1-14 ◽  
Author(s):  
Greco Hernández ◽  
Christopher G. Proud ◽  
Thomas Preiss ◽  
Armen Parsyan
Keyword(s):  
Model Organisms ◽  
Ecological Niches ◽  
Translational Machinery ◽  
Functional Differences ◽  
Profound Knowledge ◽  
Genome Wide ◽  
Translation Apparatus ◽  
Fundamental Process ◽  
Organismal Complexity ◽  
Living Organisms

Diversity is one of the most remarkable features of living organisms. Current assessments of eukaryote biodiversity reaches 1.5 million species, but the true figure could be several times that number. Diversity is ingrained in all stages and echelons of life, namely, the occupancy of ecological niches, behavioral patterns, body plans and organismal complexity, as well as metabolic needs and genetics. In this review, we will discuss that diversity also exists in a key biochemical process, translation, across eukaryotes. Translation is a fundamental process for all forms of life, and the basic components and mechanisms of translation in eukaryotes have been largely established upon the study of traditional, so-called model organisms. By using modern genome-wide, high-throughput technologies, recent studies of many nonmodel eukaryotes have unveiled a surprising diversity in the configuration of the translation apparatus across eukaryotes, showing that this apparatus is far from being evolutionarily static. For some of the components of this machinery, functional differences between different species have also been found. The recent research reviewed in this article highlights the molecular and functional diversification the translational machinery has undergone during eukaryotic evolution. A better understanding of all aspects of organismal diversity is key to a more profound knowledge of life.

scholarly journals Eutherians experienced elevated evolutionary rates in the immediate aftermath of the Cretaceous–Palaeogene mass extinction

2016 ◽  
Vol 283 (1833) ◽  
pp. 20153026 ◽  
Author(s):  
Thomas John Dixon Halliday ◽  
Paul Upchurch ◽  
Anjali Goswami
Keyword(s):  
Phylogenetic Analysis ◽  
Adaptive Radiation ◽  
Mass Extinction ◽  
Fossil Record ◽  
Morphological Evolution ◽  
Placental Mammal ◽  
Stochastic Methods ◽  
Ecological Niches ◽  
Evolutionary Radiation ◽  
Quantitative Analyses

The effect of the Cretaceous–Palaeogene (K–Pg) mass extinction on the evolution of many groups, including placental mammals, has been hotly debated. The fossil record suggests a sudden adaptive radiation of placentals immediately after the event, but several recent quantitative analyses have reconstructed no significant increase in either clade origination rates or rates of character evolution in the Palaeocene. Here we use stochastic methods to date a recent phylogenetic analysis of Cretaceous and Palaeocene mammals and show that Placentalia likely originated in the Late Cretaceous, but that most intraordinal diversification occurred during the earliest Palaeocene. This analysis reconstructs fewer than 10 placental mammal lineages crossing the K–Pg boundary. Moreover, we show that rates of morphological evolution in the 5 Myr interval immediately after the K–Pg mass extinction are three times higher than background rates during the Cretaceous. These results suggest that the K–Pg mass extinction had a marked impact on placental mammal diversification, supporting the view that an evolutionary radiation occurred as placental lineages invaded new ecological niches during the Early Palaeocene.

Treatment of Seasonal Affective Disorder with Light in the Evening

1985 ◽  
Vol 147 (4) ◽  
pp. 424-428 ◽  
Author(s):  
Steven P. James ◽  
Thomas A. Wehr ◽  
David A. Sack ◽  
Barbara L. Parry ◽  
Norman E. Rosenthal
Keyword(s):  
Sleep Deprivation ◽  
Affective Disorder ◽  
Seasonal Affective Disorder ◽  
Bright Light ◽  
Early Morning ◽  
Antidepressant Effect ◽  
Comparison Study ◽  
Female Patients ◽  
Dim Light ◽  
Effect Of Light

A cross-over comparison study of exposure, in the evenings only, to bright versus dim light was carried out on nine female patients with seasonal affective disorder. A significant antidepressant effect of the bright lights was shown. No consistent observable effects were produced by the dim lights. These results support earlier studies demonstrating the efficacy of bright light given morning and evening. The antidepressant effect of light is not mediated by sleep deprivation, and the early morning hours are not crucial for a response.

scholarly journals Origin of a major infectious disease in vertebrates: The timing of Cryptosporidium evolution and its hosts

Parasitology ◽  
2016 ◽  
Vol 143 (13) ◽  
pp. 1683-1690 ◽  
Author(s):  
JUAN C. GARCIA-R ◽  
DAVID T. S. HAYMAN
Keyword(s):  
Infectious Disease ◽  
Adaptive Radiation ◽  
Strong Support ◽  
Molecular Clocks ◽  
Protozoan Parasites ◽  
Host Shifts ◽  
Parasite Lineage ◽  
Vertebrate Hosts ◽  
Major Infectious Disease ◽  
Age Estimates

SUMMARYProtozoan parasites of the genus Cryptosporidium infect all vertebrate groups and display some host specificity in their infections. It is therefore possible to assume that Cryptosporidium parasites evolved intimately aside with vertebrate lineages. Here we propose a scenario of Cryptosporidium–Vertebrata coevolution testing the hypothesis that the origin of Cryptosporidium parasites follows that of the origin of modern vertebrates. We use calibrated molecular clocks and cophylogeny analyses to provide and compare age estimates and patterns of association between these clades. Our study provides strong support for the evolution of parasitism of Cryptosporidium with the rise of the vertebrates about 600 million years ago (Mya). Interestingly, periods of increased diversification in Cryptosporidium coincides with diversification of crown mammalian and avian orders after the Cretaceous-Palaeogene (K-Pg) boundary, suggesting that adaptive radiation to new mammalian and avian hosts triggered the diversification of this parasite lineage. Despite evidence for ongoing host shifts we also found significant correlation between protozoan parasites and vertebrate hosts trees in the cophylogenetic analysis. These results help us to understand the underlying macroevolutionary mechanisms driving evolution in Cryptosporidium and may have important implications for the ecology, dynamics and epidemiology of cryptosporidiosis disease in humans and other animals.

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