scholarly journals The coffee genome provides insight into the convergent evolution of caffeine biosynthesis

Science ◽  
2014 ◽  
Vol 345 (6201) ◽  
pp. 1181-1184 ◽  
Author(s):  
F. Denoeud ◽  
L. Carretero-Paulet ◽  
A. Dereeper ◽  
G. Droc ◽  
R. Guyot ◽  
...  
Keyword(s):  
Convergent Evolution ◽  
Caffeine Biosynthesis ◽  
Insight Into

scholarly journals Interspecies Chromosome Mapping in Caprimulgiformes, Piciformes, Suliformes, and Trogoniformes (Aves): Cytogenomic Insight into Microchromosome Organization and Karyotype Evolution in Birds

Cells ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 826
Author(s):  
Rafael Kretschmer ◽  
Marcelo Santos de Souza ◽  
Ivanete de Oliveira Furo ◽  
Michael N. Romanov ◽  
Ricardo José Gunski ◽  
...  
Keyword(s):  
Convergent Evolution ◽  
Karyotype Evolution ◽  
Rare Events ◽  
Rare Event ◽  
Chromosome Mapping ◽  
The Other ◽  
Other Hand ◽  
Interchromosomal Rearrangement ◽  
Insight Into ◽  
Phalacrocorax Brasilianus

Interchromosomal rearrangements involving microchromosomes are rare events in birds. To date, they have been found mostly in Psittaciformes, Falconiformes, and Cuculiformes, although only a few orders have been analyzed. Hence, cytogenomic studies focusing on microchromosomes in species belonging to different bird orders are essential to shed more light on the avian chromosome and karyotype evolution. Based on this, we performed a comparative chromosome mapping for chicken microchromosomes 10 to 28 using interspecies BAC-based FISH hybridization in five species, representing four Neoaves orders (Caprimulgiformes, Piciformes, Suliformes, and Trogoniformes). Our results suggest that the ancestral microchromosomal syntenies are conserved in Pteroglossus inscriptus (Piciformes), Ramphastos tucanus tucanus (Piciformes), and Trogon surrucura surrucura (Trogoniformes). On the other hand, chromosome reorganization in Phalacrocorax brasilianus (Suliformes) and Hydropsalis torquata (Caprimulgiformes) included fusions involving both macro- and microchromosomes. Fissions in macrochromosomes were observed in P. brasilianus and H. torquata. Relevant hypothetical Neognathae and Neoaves ancestral karyotypes were reconstructed to trace these rearrangements. We found no interchromosomal rearrangement involving microchromosomes to be shared between avian orders where rearrangements were detected. Our findings suggest that convergent evolution involving microchromosomal change is a rare event in birds and may be appropriate in cytotaxonomic inferences in orders where these rearrangements occurred.

scholarly journals Convergent evolution of caffeine in plants by co-option of exapted ancestral enzymes

2016 ◽  
Vol 113 (38) ◽  
pp. 10613-10618 ◽  
Author(s):  
Ruiqi Huang ◽  
Andrew J. O’Donnell ◽  
Jessica J. Barboline ◽  
Todd J. Barkman
Keyword(s):  
Genetic Diversity ◽  
Plant Defense ◽  
Plant Species ◽  
Convergent Evolution ◽  
Flowering Plant ◽  
Phylogenetic Relatedness ◽  
Future Studies ◽  
Biochemical Pathways ◽  
Caffeine Synthase ◽  
Caffeine Biosynthesis

Convergent evolution is a process that has occurred throughout the tree of life, but the historical genetic and biochemical context promoting the repeated independent origins of a trait is rarely understood. The well-known stimulant caffeine, and its xanthine alkaloid precursors, has evolved multiple times in flowering plant history for various roles in plant defense and pollination. We have shown that convergent caffeine production, surprisingly, has evolved by two previously unknown biochemical pathways in chocolate, citrus, and guaraná plants using either caffeine synthase- or xanthine methyltransferase-like enzymes. However, the pathway and enzyme lineage used by any given plant species is not predictable from phylogenetic relatedness alone. Ancestral sequence resurrection reveals that this convergence was facilitated by co-option of genes maintained over 100 million y for alternative biochemical roles. The ancient enzymes of the Citrus lineage were exapted for reactions currently used for various steps of caffeine biosynthesis and required very few mutations to acquire modern-day enzymatic characteristics, allowing for the evolution of a complete pathway. Future studies aimed at manipulating caffeine content of plants will require the use of different approaches given the metabolic and genetic diversity revealed by this study.

scholarly journals The effects of increasing the number of taxa on inferences of molecular convergence

2016 ◽  
Author(s):  
Gregg W.C. Thomas ◽  
Matthew W. Hahn ◽  
Yoonsoo Hahn
Keyword(s):  
Positive Selection ◽  
Sample Size ◽  
Comparative Studies ◽  
Convergent Evolution ◽  
Marine Mammals ◽  
Large Scale ◽  
Marine Species ◽  
Original Analysis ◽  
Insight Into ◽  
Molecular Convergence

AbstractConvergent evolution provides insight into the link between phenotype and genotype. Recently, large-scale comparative studies of convergent evolution have become possible, but researchers are still trying to determine the best way to design these types of analyses. One aspect of molecular convergence studies that has not yet been investigated is how taxonomic sample size affects inferences of molecular convergence. Here we show that increased sample size decreases the amount of inferred molecular convergence associated with the three convergent transitions to a marine environment in mammals. The sampling of more taxa—both with and without the convergent phenotype—reveals that alleles associated only with marine mammals in small datasets are actually more widespread, or are not shared by all marine species. The sampling of more taxa also allows finer resolution of ancestral substitutions, revealing that they are not in fact on lineages leading to solely marine species. We revisit a previous study on marine mammals and find that only 7 of the reported 43 genes with convergent substitutions still show signs of convergence with a larger number of background species. However, 4 of those 7 genes also showed signs of positive selection in the original analysis and may still be good candidates for adaptive convergence. Though our study is framed around the convergence of marine mammals, we expect our conclusions on taxonomic sampling are generalizable to any study of molecular convergence.

Evolution and Physiology of Amphibious Yeasts

2021 ◽  
Vol 75 (1) ◽  
Author(s):  
Fouad El Baidouri ◽  
Polona Zalar ◽  
Timothy Y. James ◽  
Amy S. Gladfelter ◽  
Anthony Amend
Keyword(s):  
Online Publication ◽  
Convergent Evolution ◽  
Annual Review ◽  
Publication Date ◽  
Ecological Diversity ◽  
Aquatic Habitats ◽  
Evolutionary Mechanisms ◽  
Unicellular Organisms ◽  
Extreme Habitats ◽  
Insight Into

Since the emergence of the first fungi some 700 million years ago, unicellular yeast-like forms have emerged multiple times in independent lineages via convergent evolution. While tens to hundreds of millions of years separate the independent evolution of these unicellular organisms, they share remarkable phenotypic and metabolic similarities, and all have streamlined genomes. Yeasts occur in every aquatic environment yet examined. Many species are aquatic; perhaps most are amphibious. How these species have evolved to thrive in aquatic habitats is fundamental to understanding functions and evolutionary mechanisms in this unique group of fungi. Here we review the state of knowledge of the physiological and ecological diversity of amphibious yeasts and their key evolutionary adaptations enabling survival in aquatic habitats. We emphasize some genera previously thought to be exclusively terrestrial. Finally, we discuss the ability of many yeasts to survive in extreme habitats and how this might lend insight into ecological plasticity, including amphibious lifestyles. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Widespread convergence in toxin resistance by predictable molecular evolution

2015 ◽  
Vol 112 (38) ◽  
pp. 11911-11916 ◽  
Author(s):  
Beata Ujvari ◽  
Nicholas R. Casewell ◽  
Kartik Sunagar ◽  
Kevin Arbuckle ◽  
Wolfgang Wüster ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Cardiac Glycoside ◽  
Convergent Evolution ◽  
Point Mutations ◽  
Sodium Potassium ◽  
Toxin Resistance ◽  
The Subject ◽  
Taxonomic Groups ◽  
Core Part ◽  
Insight Into

The question about whether evolution is unpredictable and stochastic or intermittently constrained along predictable pathways is the subject of a fundamental debate in biology, in which understanding convergent evolution plays a central role. At the molecular level, documented examples of convergence are rare and limited to occurring within specific taxonomic groups. Here we provide evidence of constrained convergent molecular evolution across the metazoan tree of life. We show that resistance to toxic cardiac glycosides produced by plants and bufonid toads is mediated by similar molecular changes to the sodium-potassium-pump (Na+/K+-ATPase) in insects, amphibians, reptiles, and mammals. In toad-feeding reptiles, resistance is conferred by two point mutations that have evolved convergently on four occasions, whereas evidence of a molecular reversal back to the susceptible state in varanid lizards migrating to toad-free areas suggests that toxin resistance is maladaptive in the absence of selection. Importantly, resistance in all taxa is mediated by replacements of 2 of the 12 amino acids comprising the Na+/K+-ATPase H1–H2 extracellular domain that constitutes a core part of the cardiac glycoside binding site. We provide mechanistic insight into the basis of resistance by showing that these alterations perturb the interaction between the cardiac glycoside bufalin and the Na+/K+-ATPase. Thus, similar selection pressures have resulted in convergent evolution of the same molecular solution across the breadth of the animal kingdom, demonstrating how a scarcity of possible solutions to a selective challenge can lead to highly predictable evolutionary responses.

scholarly journals ManyBirds: A multi-site collaborative Open Science approach to avian cognition and behaviour research

2021 ◽  
Author(s):  
Megan Lambert ◽  
Benjamin George Farrar ◽  
Elias Garcia-Pelegrin ◽  
Stephan A. Reber ◽  
Rachael Miller
Keyword(s):  
Comparative Studies ◽  
Convergent Evolution ◽  
Large Scale ◽  
Open Science ◽  
Future Directions ◽  
Avian Cognition ◽  
Current State ◽  
Science Approach ◽  
Insight Into ◽  
Representative Samples

Comparative cognitive and behaviour research aims to investigate cognitive evolution by comparing performance in different species to understand how these abilities have evolved. Ideally, this requires large and diverse samples, however, these can be difficult to obtain by single labs or institutions, leading to potential reproducibility and generalisation issues with small, less representative samples. To help mitigate these issues, we are establishing a multi-site collaborative Open Science approach called ManyBirds, with the aim of providing new insight into the evolution of avian cognition and behaviour through large-scale comparative studies, following the lead of exemplary ManyPrimates, ManyBabies and ManyDogs projects. Here, we outline a) why we should study birds, including the origin of modern birds, avian brains, convergent evolution of cognition, and the replicability crisis; b) the current state of the avian cognition field, including a ‘snapshot’ review; c) the ManyBirds project, with plans, infrastructure, limitations, implications and future directions. In sharing this process, we hope that this may be useful for other researchers in devising similar projects in other taxa, like non-avian reptiles or mammals, and to encourage further collaborations with ManyBirds and related ManyX projects. Ultimately, we hope to promote collaboration between ManyX projects to allow for wider investigation of the evolution of cognition across all animals, including potentially humans.

scholarly journals The acacia ants revisited: convergent evolution and biogeographic context in an iconic ant/plant mutualism

2017 ◽  
Vol 284 (1850) ◽  
pp. 20162569 ◽  
Author(s):  
Philip S. Ward ◽  
Michael G. Branstetter
Keyword(s):  
Central America ◽  
Convergent Evolution ◽  
Evolutionary History ◽  
Origin And Evolution ◽  
Sequence Capture ◽  
History Of ◽  
Acacia Ants ◽  
Element Sequence ◽  
Insight Into ◽  
Geographical Context

Phylogenetic and biogeographic analyses can enhance our understanding of multispecies interactions by placing the origin and evolution of such interactions in a temporal and geographical context. We use a phylogenomic approach—ultraconserved element sequence capture—to investigate the evolutionary history of an iconic multispecies mutualism: Neotropical acacia ants ( Pseudomyrmex ferrugineus group) and their associated Vachellia hostplants. In this system, the ants receive shelter and food from the host plant, and they aggressively defend the plant against herbivores and competing plants. We confirm the existence of two separate lineages of obligate acacia ants that convergently occupied Vachellia and evolved plant-protecting behaviour, from timid ancestors inhabiting dead twigs in rainforest. The more diverse of the two clades is inferred to have arisen in the Late Miocene in northern Mesoamerica, and subsequently expanded its range throughout much of Central America. The other lineage is estimated to have originated in southern Mesoamerica about 3 Myr later, apparently piggy-backing on the pre-existing mutualism. Initiation of the Pseudomyrmex / Vachellia interaction involved a shift in the ants from closed to open habitats, into an environment with more intense plant herbivory. Comparative studies of the two lineages of mutualists should provide insight into the essential features binding this mutualism.

scholarly journals Convergent Evolution of Locomotory Modes in Euarchontoglires

2020 ◽  
Vol 8 ◽  
Author(s):  
Wei-hang Geng ◽  
Xiao-ping Wang ◽  
Li-feng Che ◽  
Xin Wang ◽  
Rui Liu ◽  
...  
Keyword(s):  
Adaptive Evolution ◽  
Convergent Evolution ◽  
Proximal Phalanx ◽  
Terrestrial Species ◽  
Principle Component ◽  
Locomotory Mode ◽  
Insight Into ◽  
Phenotypic Convergence

The research of phenotypic convergence is of increasing importance in adaptive evolution. Locomotory modes play important roles in the adaptive evolution of species in the Euarchontoglires, however, the investigation of convergent evolution of the locomotory modes across diverse Euarchontoglire orders is incomplete. We collected measurements of three phalangeal indices of manual digit III, including metacarpal of digit III (MC3), manus proximal phalanx of digit III (MPP3), and manus intermediate phalanx of digit III (MIP3), from 203 individuals of 122 Euarchontoglires species representing arboreal (orders Scandentia, Rodentia, and Primates), terrestrial (orders Scandentia and Rodentia), and gliding (orders Dermoptera and Rodentia) locomotory modes. This data can be separated into seven groups defined by order and locomotory mode. Based on combination of the three phalangeal indices, the Principle component analyses (PCA), phylomorphospace plot, and C-metrics analyses clustered the arboreal species of Scandentia, Rodentia, and Primates together and the terrestrial species of Scandentia and Rodentia together, showing the convergent signal in evolution of the arboreal (C1 = 0.424, P < 0.05) and terrestrial (C1 = 0.560, P < 0.05) locomotory modes in Euarchontoglires. Although the gliding species from Dermoptera and Rodentia did not cluster together, they also showed the convergent signal (C1 = 0.563, P < 0.05). Our work provides insight into the convergent evolution of locomotory modes in Euarchontoglires, and reveals that these three indices contribute valuable information to identify convergent evolution in Euarchontoglires.

scholarly journals First evidence of convergent lifestyle signal in reptile skull roof microanatomy

BMC Biology ◽  
2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Roy Ebel ◽  
Johannes Müller ◽  
Till Ramm ◽  
Christy Hipsley ◽  
Eli Amson
Keyword(s):  
Cross Sections ◽  
Convergent Evolution ◽  
Morphological Traits ◽  
Evolutionary History ◽  
Evolutionary Mechanisms ◽  
Skull Roof ◽  
Representative Subset ◽  
Evolutionary Pathways ◽  
Fundamental Insight ◽  
Insight Into

Abstract Background The study of convergently acquired adaptations allows fundamental insight into life’s evolutionary history. Within lepidosaur reptiles—i.e. lizards, tuatara, and snakes—a fully fossorial (‘burrowing’) lifestyle has independently evolved in most major clades. However, despite their consistent use of the skull as a digging tool, cranial modifications common to all these lineages are yet to be found. In particular, bone microanatomy, although highly diagnostic for lifestyle, remains unexplored in the lepidosaur cranium. This constitutes a key gap in our understanding of their complexly interwoven ecology, morphology, and evolution. In order to bridge this gap, we reconstructed the acquisition of a fossorial lifestyle in 2813 lepidosaurs and assessed the skull roof compactness from microCT cross-sections in a representative subset (n = 99). We tested this and five macroscopic morphological traits for their convergent evolution. Results We found that fossoriality evolved independently in 54 lepidosaur lineages. Furthermore, a highly compact skull roof, small skull diameter, elongate cranium, and low length ratio of frontal and parietal were repeatedly acquired in concert with a fossorial lifestyle. Conclusions We report a novel case of convergence that concerns lepidosaur diversity as a whole. Our findings further indicate an early evolution of fossorial modifications in the amphisbaenian ‘worm-lizards’ and support a fossorial origin for snakes. Nonetheless, our results suggest distinct evolutionary pathways between fossorial lizards and snakes through different contingencies. We thus provide novel insights into the evolutionary mechanisms and constraints underlying amniote diversity and a powerful tool for the reconstruction of extinct reptile ecology.

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