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.

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 Out of the blue: adaptive visual pigment evolution accompanies Amazon invasion

2015 ◽  
Vol 11 (7) ◽  
pp. 20150349 ◽  
Author(s):  
Alexander Van Nynatten ◽  
Devin Bloom ◽  
Belinda S. W. Chang ◽  
Nathan R. Lovejoy
Keyword(s):  
Molecular Evolution ◽  
Positive Selection ◽  
Visual Pigment ◽  
Large Scale ◽  
Marine Species ◽  
South American ◽  
Sequence Analyses ◽  
Freshwater Habitats ◽  
Varying Environments ◽  
Visual Pigment Evolution

Incursions of marine water into South America during the Miocene prompted colonization of freshwater habitats by ancestrally marine species and present a unique opportunity to study the molecular evolution of adaptations to varying environments. Freshwater and marine environments are distinct in both spectra and average intensities of available light. Here, we investigate the molecular evolution of rhodopsin, the photosensitive pigment in the eye that activates in response to light, in a clade of South American freshwater anchovies derived from a marine ancestral lineage. Using likelihood-based comparative sequence analyses, we found evidence for positive selection in the rhodopsin of freshwater anchovy lineages at sites known to be important for aspects of rhodopsin function such as spectral tuning. No evidence was found for positive selection in marine lineages, nor in three other genes not involved in vision. Our results suggest that an increased rate of rhodopsin evolution was driven by diversification into freshwater habitats, thereby constituting a rare example of molecular evolution mirroring large-scale palaeogeographic events.

scholarly journals The Parallel Molecular Adaptations to the Antarctic Cold Environment in Two Psychrophilic Green Algae

2019 ◽  
Vol 11 (7) ◽  
pp. 1897-1908 ◽  
Author(s):  
Zhenhua Zhang ◽  
Changfeng Qu ◽  
Ru Yao ◽  
Yuan Nie ◽  
Chenjie Xu ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Positive Selection ◽  
Green Algae ◽  
Large Scale ◽  
Extreme Environments ◽  
Photosynthetic Apparatus ◽  
Antioxidant Systems ◽  
Significant Evidence ◽  
The Antarctic ◽  
Molecular Convergence

Abstract Psychrophilic green algae from independent phylogenetic lines thrive in the polar extreme environments, but the hypothesis that their psychrophilic characteristics appeared through parallel routes of molecular evolution remains untested. The recent surge of transcriptome data enables large-scale evolutionary analyses to investigate the genetic basis for the adaptations to the Antarctic extreme environment, and the identification of the selective forces that drive molecular evolution is the foundation to understand the strategies of cold adaptation. Here, we conducted transcriptome sequencing of two Antarctic psychrophilic green algae (Chlamydomonas sp. ICE-L and Tetrabaena socialis) and performed positive selection and convergent substitution analyses to investigate their molecular convergence and adaptive strategies against extreme cold conditions. Our results revealed considerable shared positively selected genes and significant evidence of molecular convergence in two Antarctic psychrophilic algae. Significant evidence of positive selection and convergent substitution were detected in genes associated with photosynthetic machinery, multiple antioxidant systems, and several crucial translation elements in Antarctic psychrophilic algae. Our study reveals that the psychrophilic algae possess more stable photosynthetic apparatus and multiple protective mechanisms and provides new clues of parallel adaptive evolution in Antarctic psychrophilic green algae.

scholarly journals Convergent genomic signatures of high-altitude adaptation among domestic mammals

2019 ◽  
Vol 7 (6) ◽  
pp. 952-963 ◽  
Author(s):  
Dong-Dong Wu ◽  
Cui-Ping Yang ◽  
Ming-Shan Wang ◽  
Kun-Zhe Dong ◽  
Da-Wei Yan ◽  
...  
Keyword(s):  
Positive Selection ◽  
High Altitude ◽  
Adaptive Evolution ◽  
The Tibetan Plateau ◽  
Genomic Signatures ◽  
Gene Level ◽  
Genetic Mechanisms ◽  
Altitude Adaptation ◽  
Insight Into ◽  
Molecular Convergence

Abstract Abundant and diverse domestic mammals living on the Tibetan Plateau provide useful materials for investigating adaptive evolution and genetic convergence. Here, we used 327 genomes from horses, sheep, goats, cattle, pigs and dogs living at both high and low altitudes, including 73 genomes generated for this study, to disentangle the genetic mechanisms underlying local adaptation of domestic mammals. Although molecular convergence is comparatively rare at the DNA sequence level, we found convergent signature of positive selection at the gene level, particularly the EPAS1 gene in these Tibetan domestic mammals. We also reported a potential function in response to hypoxia for the gene C10orf67, which underwent positive selection in three of the domestic mammals. Our data provide an insight into adaptive evolution of high-altitude domestic mammals, and should facilitate the search for additional novel genes involved in the hypoxia response pathway.

scholarly journals Convergent genomic signatures of high altitude adaptation among domestic mammals

2019 ◽  
Author(s):  
Dong-Dong Wu ◽  
Cui-Ping Yang ◽  
Ming-Shan Wang ◽  
Kun-Zhe Dong ◽  
Da-Wei Yan ◽  
...  
Keyword(s):  
Positive Selection ◽  
High Altitude ◽  
Adaptive Evolution ◽  
The Tibetan Plateau ◽  
Genomic Signatures ◽  
Gene Level ◽  
Genetic Mechanisms ◽  
Altitude Adaptation ◽  
Insight Into ◽  
Molecular Convergence

AbstractAbundant and diverse domestic mammals living on the Tibetan Plateau provide useful materials for investigating adaptive evolution and genetic convergence. Here, we utilized 327 genomes from horses, sheep, goats, cattle, pigs and dogs living at both high and low altitudes, including 73 genomes generated for this study, to disentangle the genetic mechanisms underlying local adaptation of domestic mammals. Although molecular convergence is comparatively rare at the DNA sequence level, we found convergent signature of positive selection at the gene level, particularly EPAS1 gene in these Tibetan domestic mammals. We also reported a potential function in response to hypoxia for the gene C10orf67, which underwent positive selection in three of the domestic mammals. Our data provides insight into adaptive evolution of high-altitude domestic mammals, and should facilitate the search for additional novel genes involved in the hypoxia response pathway.

scholarly journals Predicting sample success for large‐scale ancient DNA studies on marine mammals

2021 ◽  
Author(s):  
Xénia Keighley ◽  
Maiken Hemme Bro‐Jørgensen ◽  
Hans Ahlgren ◽  
Paul Szpak ◽  
Marta Maria Ciucani ◽  
...  
Keyword(s):  
Ancient Dna ◽  
Marine Mammals ◽  
Large Scale

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.

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