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| 2. |
- Feng, Shaohong, et al.
(författare)
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Dense sampling of bird diversity increases power of comparative genomics
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 587:7833
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Tidskriftsartikel (refereegranskat)abstract
- Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
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| 3. |
- Pease, J. B., et al.
(författare)
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Layered evolution of gene expression in "superfast" muscles for courtship
- 2022
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Ingår i: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. - : Proceedings of the National Academy of Sciences. - 0027-8424. ; 119:14
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Tidskriftsartikel (refereegranskat)abstract
- Identifying the molecular process of complex trait evolution is a core goal of biology. However, pinpointing the specific context and timing of trait-associated changes within the molecular evolutionary history of an organism remains an elusive goal. We study this topic by exploring the molecular basis of elaborate courtship evolution, which represents an extraordinary example of trait innovation. Within the behaviorally diverse radiation of Central and South American manakin birds, species from two separate lineages beat their wings together using specialized "superfast" muscles to generate a "snap" that helps attract mates. Here, we develop an empirical approach to analyze phylogenetic lineage-specific shifts in gene expression in the key snap-performing muscle and then integrate these findings with comparative transcriptomic sequence analysis. We find that rapid wing displays are associated with changes to a wide range of molecular processes that underlie extreme muscle performance, including changes to calcium trafficking, myocyte homeostasis and metabolism, and hormone action. We furthermore show that these changes occur gradually in a layered manner across the species history, wherein which ancestral genetic changes to many of these molecular systems are built upon by later species-specific shifts that likely finalized the process of display performance adaptation. Our study demonstrates the potential for combining phylogenetic modeling of tissue-specific gene expression shifts with phylogenetic analysis of lineage-specific sequence changes to reveal holistic evolutionary histories of complex traits.
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| 4. |
- Friscia, A., et al.
(författare)
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Adaptive Evolution of a Derived Radius Morphology in Manakins (Aves, Pipridae) to Support Acrobatic Display Behavior
- 2016
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Ingår i: Journal of Morphology. - : Wiley. - 0362-2525. ; 277:6, s. 766-775
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Tidskriftsartikel (refereegranskat)abstract
- The morphology of the avian skeleton is often studied in the context of adaptations for powered flight. The effects of other evolutionary forces, such as sexual selection, on avian skeletal design are unclear, even though birds produce diverse behaviors that undoubtedly require a variety of osteological modifications. Here, we investigate this issue in a family of passerine birds called manakins (Pipridae), which have evolved physically unusual and elaborate courtship displays. We report that, in species within the genus Manacus, the shaft of the radius is heavily flattened and shows substantial solidification. Past work anecdotally notes this morphology and attributes it to the species' ability to hit their wings together above their heads to produce loud mechanical sonations. Our results show that this feature is unique to Manacus compared to the other species in our study, including a variety of taxa that produce other sonations through alternate wing mechanisms. At the same time, our data reveal striking similarities across species in total radius volume and solidification. Together, this suggests that supposedly adaptive alterations in radial morphology occur within a conserved framework of a set radius volume and solidness, which in turn is likely determined by natural selection. Further allometric analyses imply that the radius is less constrained by body size and the structural demands that underlie powered flight, compared to other forelimb bones that are mostly unmodified across taxa. These results are consistent with the idea that the radius is more susceptible to selective modification by sexual selection. Overall, this study provides some of the first insight into the osteological evolution of passerine birds, as well as the way in which opposing selective forces can shape skeletal design in these species. (C) 2016 Wiley Periodicals, Inc.
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| 5. |
- Fuxjager, M. J., et al.
(författare)
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Evolutionary patterns of adaptive acrobatics and physical performance predict expression profiles of androgen receptor - but not oestrogen receptor - in the forelimb musculature
- 2015
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Ingår i: Functional Ecology. - : Wiley. - 0269-8463 .- 1365-2435. ; 29:9, s. 1197-1208
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Tidskriftsartikel (refereegranskat)abstract
- Superior physical competence is vital to the adaptive behavioural routines of many animals, particularly those that engage in elaborate sociosexual displays. How such traits evolve across species remains unclear. Recent work suggests that activation of sex steroid receptors in neuromuscular systems is necessary for the fine motor skills needed to execute physically elaborate displays. Thus, using passerine birds as models, we test whether interspecific variation in display complexity predicts species differences in the abundance of androgen and oestrogen receptors (AR and ER-) expressed in the forelimb musculature and spinal cord. We find that small-scale evolutionary patterns in physical display complexity positively predict expression of AR in the main muscles that lift and retract the wings. No such relationship is detected in the spinal cord, and we do not find a correlation between display behaviour and neuromuscular expression of ER-. Also, we find that AR expression levels in different androgen targets throughout the body - namely the wing muscles, spinal cord and testes - are not necessarily correlated, providing evidence that evolutionary forces drive AR expression in a tissue-specific manner. These results suggest co-evolution between the physical prowess necessary for display performance and levels of AR expression in avian forelimb muscles. Moreover, this relationship appears to be both specific to muscle and AR-mediated signalling. Given that prior work suggests that activation of muscular AR is a necessary component of physical display performance, our current data support the hypothesis that sexual selection shapes levels of AR expressed in the forelimb skeletal muscles to help drive the evolution of adaptive motor abilities.
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| 6. |
- Künstner, Axel, et al.
(författare)
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Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species
- 2010
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Ingår i: Molecular Ecology. - 0962-1083 .- 1365-294X. ; 19:Suppl.1, s. 266-276
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Tidskriftsartikel (refereegranskat)abstract
- Next-generation sequencing technology provides an attractive means to obtain largescale sequence data necessary for comparative genomic analysis. To analyse the patterns of mutation rate variation and selection intensity across the avian genome, we performed brain transcriptome sequencing using Roche 454 technology of 10 different non-model avian species. Contigs from de novo assemblies were aligned to the two available avian reference genomes, chicken and zebra finch. In total, we identified 6499 different genes across all 10 species, with ∼1000 genes found in each full run per species. We found evidence for a higher mutation rate of the Z chromosome than of autosomes (male-biased mutation) and a negative correlation between the neutral substitution rate (dS) and chromosome size. Analyses of the mean dN/dS ratio (ω) of genes across chromosomes supported the Hill-Robertson effect (the effect of selection at linked loci) and point at stochastic problems with x as an independent measure of selection. Overall, this study demonstrates the usefulness of next-generation sequencing for obtaining genomic resources for comparative genomic analysis of non-model organisms.
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