| 1. |
- Blom, Mozes P. K., et al.
(author)
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Hybridization in birds-of-paradise : Widespread ancestral gene flow despite strong sexual selection in a lek-mating system
- 2024
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In: iScience. - : Cell Press. - 2589-0042. ; 27:7
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Journal article (peer-reviewed)abstract
- Sexual selection can directly contribute to reproductive isolation and is an important mechanism that can lead to speciation. Lek-mating is one of the most extreme forms of sexual selection, but surprisingly does not seem to preclude occasional hybridization in nature. However, hybridization among lekking species may still be trivial if selection against offspring with intermediate phenotypes prohibits introgression. Here we investigate this further by sequencing the genomes of nearly all bird-of-paradise (Paradisaeidae) species and 10 museum specimens of putative hybrid origin. We find that intergeneric hybridization indeed still takes place despite extreme differentiation in form, plumage, and behavior. In parallel, the genomes of contemporary species contain widespread signatures of past introgression, demonstrating that hybridization has repeatedly resulted in shared genetic variation despite strong sexual isolation. Our study raises important questions about extrinsic factors that modulate hybridization probability and the evolutionary consequences of introgressive hybridization between lekking species.
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| 2. |
- Christmas, Matthew, et al.
(author)
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Genetic Barriers to Historical Gene Flow between Cryptic Species of Alpine Bumblebees Revealed by Comparative Population Genomics
- 2021
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In: Molecular biology and evolution. - : Oxford University Press. - 0737-4038 .- 1537-1719. ; 38:8, s. 3126-3143
-
Journal article (peer-reviewed)abstract
- Evidence is accumulating that gene flow commonly occurs between recently diverged species, despite the existence of barriers to gene flow in their genomes. However, we still know little about what regions of the genome become barriers to gene flow and how such barriers form. Here, we compare genetic differentiation across the genomes of bumblebee species living in sympatry and allopatry to reveal the potential impact of gene flow during species divergence and uncover genetic barrier loci. We first compared the genomes of the alpine bumblebee Bombus sylvicola and a previously unidentified sister species living in sympatry in the Rocky Mountains, revealing prominent islands of elevated genetic divergence in the genome that colocalize with centromeres and regions of low recombination. This same pattern is observed between the genomes of another pair of closely related species living in allopatry (B. bifarius and B. vancouverensis). Strikingly however, the genomic islands exhibit significantly elevated absolute divergence (d(XY)) in the sympatric, but not the allopatric, comparison indicating that they contain loci that have acted as barriers to historical gene flow in sympatry. Our results suggest that intrinsic barriers to gene flow between species may often accumulate in regions of low recombination and near centromeres through processes such as genetic hitchhiking, and that divergence in these regions is accentuated in the presence of gene flow.
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| 3. |
- Gemmell, Neil J., et al.
(author)
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The tuatara genome reveals ancient features of amniote evolution
- 2020
-
In: Nature. - : Springer Nature. - 0028-0836 .- 1476-4687. ; 584:7821, s. 403-409
-
Journal article (peer-reviewed)abstract
- The tuatara (Sphenodon punctatus)—the only living member of the reptilian order Rhynchocephalia (Sphenodontia), once widespread across Gondwana1,2—is an iconic species that is endemic to New Zealand2,3. A key link to the now-extinct stem reptiles (from which dinosaurs, modern reptiles, birds and mammals evolved), the tuatara provides key insights into the ancestral amniotes2,4. Here we analyse the genome of the tuatara, which—at approximately 5 Gb—is among the largest of the vertebrate genomes yet assembled. Our analyses of this genome, along with comparisons with other vertebrate genomes, reinforce the uniqueness of the tuatara. Phylogenetic analyses indicate that the tuatara lineage diverged from that of snakes and lizards around 250 million years ago. This lineage also shows moderate rates of molecular evolution, with instances of punctuated evolution. Our genome sequence analysis identifies expansions of proteins, non-protein-coding RNA families and repeat elements, the latter of which show an amalgam of reptilian and mammalian features. The sequencing of the tuatara genome provides a valuable resource for deep comparative analyses of tetrapods, as well as for tuatara biology and conservation. Our study also provides important insights into both the technical challenges and the cultural obligations that are associated with genome sequencing.
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| 4. |
- Goubert, Clement, et al.
(author)
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A beginner's guide to manual curation of transposable elements
- 2022
-
In: Mobile DNA. - : Springer Nature. - 1759-8753. ; 13
-
Journal article (peer-reviewed)abstract
- Background: In the study of transposable elements (TEs), the generation of a high confidence set of consensus sequences that represent the diversity of TEs found in a given genome is a key step in the path to investigate these fascinating genomic elements. Many algorithms and pipelines are available to automatically identify putative TE families present in a genome. Despite the availability of these valuable resources, producing a library of high-quality full-length TE consensus sequences largely remains a process of manual curation. This know-how is often passed on from mentor-to-mentee within research groups, making it difficult for those outside the field to access this highly specialised skill.Results: Our manuscript attempts to fill this gap by providing a set of detailed computer protocols, software recommendations and video tutorials for those aiming to manually curate TEs. Detailed step-by-step protocols, aimed at the complete beginner, are presented in the Supplementary Methods.Conclusions: The proposed set of programs and tools presented here will make the process of manual curation achievable and amenable to all researchers and in special to those new to the field of TEs.
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| 5. |
- Guichard, Etienne, et al.
(author)
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Impact of non-LTR retrotransposons in the differentiation and evolution of anatomically modern humans
- 2018
-
In: Mobile DNA. - : BMC. - 1759-8753. ; 9
-
Journal article (peer-reviewed)abstract
- Background: Transposable elements are biologically important components of eukaryote genomes. In particular, non-LTR retrotransposons (N-LTRrs) played a key role in shaping the human genome throughout evolution. In this study, we compared retrotransposon insertions differentially present in the genomes of Anatomically Modern Humans, Neanderthals, Denisovans and Chimpanzees, in order to assess the possible impact of retrotransposition in the differentiation of the human lineage. Results: We first identified species-specific N-LTRrs and established their distribution in present day human populations. These analyses shortlisted a group of N-LTRr insertions that were found exclusively in Anatomically Modern Humans. These insertions are associated with an increase in the number of transcriptional/splicing variants of those genes they inserted in. The analysis of the functionality of genes containing human-specific N-LTRr insertions reflects changes that occurred during human evolution. In particular, the expression of genes containing the most recent N-LTRr insertions is enriched in the brain, especially in undifferentiated neurons, and these genes associate in networks related to neuron maturation and migration. Additionally, we identified candidate N-LTRr insertions that have likely produced new functional variants exclusive to modern humans, whose genomic loci show traces of positive selection. Conclusions: Our results strongly suggest that N-LTRr impacted our differentiation as a species, most likely inducing an increase in neural complexity, and have been a constant source of genomic variability all throughout the evolution of the human lineage.
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| 6. |
- Huang, Zhen, et al.
(author)
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Recurrent chromosome reshuffling and the evolution of neo-sex chromosomes in parrots
- 2022
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In: Nature Communications. - : Springer Nature. - 2041-1723. ; 13:1
-
Journal article (peer-reviewed)abstract
- Parrots have undergone substantial karyotype evolution compared to most other birds. Here, Huang et al. analyze chromosome-level genome assemblies for four parrot species and elucidate the complex evolutionary history of parrot chromosomes. The karyotype of most birds has remained considerably stable during more than 100 million years' evolution, except for some groups, such as parrots. The evolutionary processes and underlying genetic mechanism of chromosomal rearrangements in parrots, however, are poorly understood. Here, using chromosome-level assemblies of four parrot genomes, we uncover frequent chromosome fusions and fissions, with most of them occurring independently among lineages. The increased activities of chromosomal rearrangements in parrots are likely associated with parrot-specific loss of two genes, ALC1 and PARP3, that have known functions in the repair of double-strand breaks and maintenance of genome stability. We further find that the fusion of the ZW sex chromosomes and chromosome 11 has created a pair of neo-sex chromosomes in the ancestor of parrots, and the chromosome 25 has been further added to the sex chromosomes in monk parakeet. Together, the combination of our genomic and cytogenetic analyses characterizes the complex evolutionary history of chromosomal rearrangements and sex chromosomes in parrots.
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| 7. |
- Nguyen, Diem, PhD, et al.
(author)
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Transposon- and Genome Dynamics in the Fungal Genus Neurospora: Insights from Nearly Gapless Genome Assemblies
- 2022
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In: Fungal Genetics Reports. - : New Prairie Press. - 1941-4765. ; 66:1
-
Journal article (peer-reviewed)abstract
- A large portion of nuclear DNA is composed of transposable element (TE) sequences, whose transposition is controlled by diverse host defense strategies in order to maintain genomic integrity. One such strategy is the fungal-specific Repeat-Induced Point mutation (RIP) that hyper-mutates repetitive DNA sequences. While RIP is found across Fungi, it has been shown to vary in efficiency. The filamentous ascomycete Neurospora crassa has been a pioneer in the study of RIP, but data on TEs and RIP from other species in the genus is limited. In this study, we investigated 18 nearly gapless genome assemblies of ten Neurospora species, which diverged from a common ancestor about 7 MYA, to determine and compare genome-wide TE distribution and their associated RIP patterns. Four of these assemblies, generated by PacBio technology, represent new genomic datasets. We showed that the TE contents (8.7-18.9%) covary with genome sizes that range between 37.8-43.9 Mb. Degraded copies of Long Terminal Repeat (LTR) retrotransposons were abundant among the identified TEs, and these are distributed across the genome at varying frequencies. In all investigated Neurospora genomes, TE sequences had signs of numerous C-to-T substitutions, suggesting that RIP occurred in all species, and accordingly, RIP signatures correlated with TE-dense regions in all genomes. In conclusion, essentially gapless genome assemblies allowed us to identify TEs in Neurospora genomes, and reveal that TEs contribute to genome size variation in this group. Our study suggests that TEs and RIP are highly correlated in each examined Neurospora species, and hence, the pattern of interaction is conserved over the investigated evolutionary timescale. Finally, with our results, we verify that RIP signatures can be used to facilitate the identification of TE-rich regions in the genome. The comprehensive genomic dataset of Neurospora is a rich resource for further in- depth analyses of fungal genomes by the community.
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| 8. |
- Peona, Valentina, et al.
(author)
-
An annotated chromosome-scale reference genome for Eastern black-eared wheatear (Oenanthe melanoleuca)
- 2023
-
In: G3. - : Oxford University Press. - 2160-1836. ; 13:6
-
Journal article (peer-reviewed)abstract
- Pervasive convergent evolution and in part high incidences of hybridization distinguish wheatears (songbirds of the genus Oenanthe) as a versatile system to address questions at the forefront of research on the molecular bases of phenotypic and species diversification. To prepare the genomic resources for this venture, we here generated and annotated a chromosome-scale assembly of the Eastern black-eared wheatear (Oenanthe melanoleuca). This species is part of the Oenanthe hispanica complex that is characterized by convergent evolution of plumage coloration and high rates of hybridization. The long-read-based male nuclear genome assembly comprises 1.04 Gb in 32 autosomes, the Z chromosome, and the mitogenome. The assembly is highly contiguous (contig N50, 12.6 Mb; scaffold N50, 70 Mb), with 96% of the genome assembled at the chromosome level and 95.5% benchmarking universal single-copy orthologs (BUSCO) completeness. The nuclear genome was annotated with 18,143 protein-coding genes and 31,333 mRNAs (annotation BUSCO completeness, 98.0%), and about 10% of the genome consists of repetitive DNA. The annotated chromosome-scale reference genome of Eastern black-eared wheatear provides a crucial resource for research into the genomics of adaptation and speciation in an intriguing group of passerines.
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| 9. |
- Peona, Valentina, et al.
(author)
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How complete are "complete" genome assemblies? : An avian perspective
- 2018
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In: Molecular Ecology Resources. - : John Wiley & Sons. - 1755-098X .- 1755-0998. ; 18:6, s. 1188-1195
-
Journal article (peer-reviewed)abstract
- The genomics revolution has led to the sequencing of a large variety of non-model organisms often referred to as 'whole' or 'complete' genome assemblies. But how complete are these, really? Here we use birds as an example for non-model vertebrates and find that, although suitable in principle for genomic studies, the current standard of short-read assemblies misses a significant proportion of the expected genome size (7 to 42%; mean 20 ± 9%). In particular, regions with strongly deviating nucleotide composition (e.g., guanine-cytosine-[GC]-rich) and regions highly enriched in repetitive DNA (e.g., transposable elements and satellite DNA) are usually underrepresented in assemblies. However, long-read sequencing technologies successfully characterize many of these underrepresented GC-rich or repeat-rich regions in several bird genomes. For instance, only ~2% of the expected total base pairs are missing in the last chicken reference (galGal5). These assemblies still contain thousands of gaps (i.e., fragmented sequences) because some chromosomal structures (e.g., centromeres) likely contain arrays of repetitive DNA that are too long to bridge with currently available technologies. We discuss how to minimize the number of assembly gaps by combining the latest available technologies with complementary strengths. Finally, we emphasize the importance of knowing the location, size, and potential content of assembly gaps when making population genetic inferences about adjacent genomic regions.
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| 10. |
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| 11. |
- Peona, Valentina, et al.
(author)
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Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird‐of‐paradise
- 2020
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In: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 21:1, s. 263-286
-
Journal article (peer-reviewed)abstract
- Genome assemblies are currently being produced at an impressive rate by consortia and individual laboratories. The low costs and increasing efficiency of sequencing technologies now enable assembling genomes at unprecedented quality and contiguity. However, the difficulty in assembling repeat-rich and GC-rich regions (genomic “dark matter”) limits insights into the evolution of genome structure and regulatory networks. Here, we compare the efficiency of currently available sequencing technologies (short/linked/long reads and proximity ligation maps) and combinations thereof in assembling genomic dark matter. By adopting different de novo assembly strategies, we compare individual draft assemblies to a curated multiplatform reference assembly and identify the genomic features that cause gaps within each assembly. We show that a multiplatform assembly implementing long-read, linked-read and proximity sequencing technologies performs best at recovering transposable elements, multicopy MHC genes, GC-rich microchromosomes and the repeat-rich W chromosome. Telomere-to-telomere assemblies are not a reality yet for most organisms, but by leveraging technology choice it is now possible to minimize genome assembly gaps for downstream analysis. We provide a roadmap to tailor sequencing projects for optimized completeness of both the coding and noncoding parts of nonmodel genomes.
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| 12. |
- Peona, Valentina, et al.
(author)
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Satellite DNA evolution in Corvides inferred from short and long reads
-
Other publication (other academic/artistic)abstract
- Satellite DNA (satDNA) is a fast-evolving portion of eukaryotic genomes. The homogeneous and repetitive nature of such satellitomes causes problems during the assembly of genomes, and therefore it is still difficult to study satDNA in detail in non-model organisms as well as across broad evolutionary timescales. Here, we combined the use of short-read and long-read data to explore the diversity and evolution of satDNA between individuals of the same species and between genera of birds spanning ~40 millions of years of bird evolution using birds-of-paradise and Corvus species. These avian species highlighted the presence of a GC-rich Corvides satellitome composed of 61 satellite families and provided a set of candidates satDNA monomers for being centromeric on the basis of length, abundance, homogeneity and transcription. Surprisingly, we found that the satellitome of Corvus spp. rapidly diverged between closely related species while the satellitome appeared more similar between birds-of-paradise species belonging to different genera.
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| 13. |
- Peona, Valentina, et al.
(author)
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Satellite DNA evolution in Corvoidea inferred from short and long reads
- 2023
-
In: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 32:6, s. 1288-1305
-
Journal article (peer-reviewed)abstract
- Satellite DNA (satDNA) is a fast-evolving portion of eukaryotic genomes. The homogeneous and repetitive nature of such satDNA causes problems during the assembly of genomes, and therefore it is still difficult to study it in detail in nonmodel organisms as well as across broad evolutionary timescales. Here, we combined the use of short- and long-read data to explore the diversity and evolution of satDNA between individuals of the same species and between genera of birds spanning ~40 millions of years of bird evolution using birds-of-paradise (Paradisaeidae) and crow (Corvus) species. These avian species highlighted the presence of a GC-rich Corvoidea satellitome composed of 61 satellite families and provided a set of candidate satDNA monomers for being centromeric on the basis of length, abundance, homogeneity and transcription. Surprisingly, we found that the satDNA of crow species rapidly diverged between closely related species while the satDNA appeared more similar between birds-of-paradise species belonging to different genera.
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| 14. |
- Peona, Valentina, et al.
(author)
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Teaching transposon classification as a means to crowd source the curation of repeat annotation : a tardigrade perspective
- 2024
-
In: Mobile DNA. - : BioMed Central (BMC). - 1759-8753. ; 15:1
-
Journal article (peer-reviewed)abstract
- BackgroundThe advancement of sequencing technologies results in the rapid release of hundreds of new genome assemblies a year providing unprecedented resources for the study of genome evolution. Within this context, the significance of in-depth analyses of repetitive elements, transposable elements (TEs) in particular, is increasingly recognized in understanding genome evolution. Despite the plethora of available bioinformatic tools for identifying and annotating TEs, the phylogenetic distance of the target species from a curated and classified database of repetitive element sequences constrains any automated annotation effort. Moreover, manual curation of raw repeat libraries is deemed essential due to the frequent incompleteness of automatically generated consensus sequences.ResultsHere, we present an example of a crowd-sourcing effort aimed at curating and annotating TE libraries of two non-model species built around a collaborative, peer-reviewed teaching process. Manual curation and classification are time-consuming processes that offer limited short-term academic rewards and are typically confined to a few research groups where methods are taught through hands-on experience. Crowd-sourcing efforts could therefore offer a significant opportunity to bridge the gap between learning the methods of curation effectively and empowering the scientific community with high-quality, reusable repeat libraries.ConclusionsThe collaborative manual curation of TEs from two tardigrade species, for which there were no TE libraries available, resulted in the successful characterization of hundreds of new and diverse TEs in a reasonable time frame. Our crowd-sourcing setting can be used as a teaching reference guide for similar projects: A hidden treasure awaits discovery within non-model organisms.
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| 15. |
- Peona, Valentina, 1990-, et al.
(author)
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The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities
- 2021
-
In: Philosophical Transactions of the Royal Society of London. Biological Sciences. - : Royal Society. - 0962-8436 .- 1471-2970. ; 376:1833
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Journal article (peer-reviewed)abstract
- It is a broadly observed pattern that the non-recombining regions of sex- limited chromosomes (Y and W) accumulate more repeats than the rest of the genome, even in species like birds with a low genome-wide repeat content. Here, we show that in birds with highly heteromorphic sex chromosomes, the W chromosome has a transposable element (TE) density of greater than 55% compared to the genome-wide density of less than 10%, and contains over half of all full-length (thus potentially active) endogenous retroviruses (ERVs) of the entire genome. Using RNA-seq and protein mass spectrometry data, we were able to detect signatures of female-specific ERV expression. We hypothesize that the avian W chromosome acts as a refugium for active ERVs, probably leading to female-biased mutational load that may influence female physiology similar to the ‘toxic-Y’ effect in Drosophila males. Furthermore, Haldane’s rule predicts that the heterogametic sex has reduced fertility in hybrids. We propose that the excess of W-linked active ERVs over the rest of the genome may be an additional explanatory variable for Haldane’s rule, with consequences for genetic incompatibilities between species through TE/repressor mismatches in hybrids. Together, our results suggest that the sequence content of female-specific W chromosomes can have effects far beyond sex determination and gene dosage.This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)’.
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| 16. |
- Peona, Valentina, 1990-
(author)
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The exploration and evolution of the avian genomic dark matter
- 2021
-
Doctoral thesis (other academic/artistic)abstract
- The development and improvement of genome sequencing technologies in the last decade revolutionised the entire field of biology with genome assemblies of virtually any organism. Despite this tremendous progress, complex genomic regions are systematically missing from genome assemblies and form the so-called "genomic dark matter". The presence of genomic dark matter entails that such regions cannot be fully studied and the effects and/or functions thereof (if any) on the organisms remain hidden. Therefore, it is key to be able to explore those dark genomic corners to fully understand the evolution and physiology of organisms without biasing the interpretations. In this thesis, I contribute to the understanding of the use of new sequencing technologies to assemble complex genomic regions and to investigate the evolution of such regions throughout the avian phylogeny. First, I assessed the best combination of technologies and assembly methods to maximise the resolution of genomic dark matter using genomic data from the paradise crow. This included testing for the presence of repetitive elements, GC-rich regions, G-quadruplex motifs, non-recombining sex chromosomes, and microchromosomes. Then, the high-quality assemblies for the paradise crow and other birds allowed the discovery that the avian W chromosome features more than half of potentially active transposable elements (TEs), especially endogenous retroviruses, of the genome. This characteristic makes the W chromosome potentially "toxic" for females. The female-biased accumulation of active TEs could also play a role in the origin of genetic incompatibilities and be an explanatory variable for Haldane’s rule in birds. Next, I investigated the genetic variability of birds-of-paradise chromosomes originating from structural rearrangements with a special focus on the W chromosome. The analysis revealed more genetic variability than previously reported suggesting that all sources of genetic variability should be considered to understand the evolution of sex-limited chromosomes. Finally, I explored the evolution of another main component of avian genomic dark matter, satellite DNA, throughout the phylogeny of birds-of-paradise and closely related crow species. I found that the avian satellitome evolves in different modes in the two groups and a more comprehensive species sampling is necessary to establish which evolutionary mode is the most prevalent in birds. Altogether, the results of this thesis provide a case study for how to investigate the most complex genomic regions, highlight their possible evolutionary roles, and therefore showcase the necessity for the field to shed light into the dark corners of genomes. Mind the gap!
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| 17. |
- Peona, Valentina, et al.
(author)
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The hidden structural variability in avian genomes
-
Other publication (other academic/artistic)abstract
- Structural variants (SVs) are DNA mutations that can have relevant effects at the micro- and macro-evolutionary scales. The detection of SVs is largely limited by the type and quality of sequencing technologies adopted, therefore genetic variability linked to SVs may remain undiscovered especially in complex repetitive regions. In this study, we used a combination of long-read and linked-read genome assemblies to explore the occurrence of insertions and deletions across the chromosomes of 14 species birds-of-paradise and two species of estrildid finches. The species sampling encompasses all genera of birds-of-paradise, allowing comparisons between individuals of the same species, genus, and family. Interestingly, we found the highest densities of SVs to be located on the microchromosomes and on the female-specific W chromosome. Genome assemblies of multiple individuals from the same species allowed us to compare the levels of genetic variability linked to SVs and single nucleotide polymorphisms (SNPs) on the W and other chromosomes. Our results demonstrate that the avian W chromosome harbours more genetic variability than previously thought and that its structure is shaped by the continuous accumulation and turnover of transposable element insertions, especially endogenous retroviruses.
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| 18. |
- Ricci, Marco, et al.
(author)
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Comparative analysis of bats and rodents' genomes suggests a relation between non-LTR retrotransposons, cancer incidence, and ageing
- 2023
-
In: Scientific Reports. - : Springer Nature. - 2045-2322. ; 13:1
-
Journal article (peer-reviewed)abstract
- The presence in nature of species showing drastic differences in lifespan and cancer incidence has recently increased the interest of the scientific community. In particular, the adaptations and the genomic features underlying the evolution of cancer-resistant and long-lived organisms have recently focused on transposable elements (TEs). In this study, we compared the content and dynamics of TE activity in the genomes of four rodent and six bat species exhibiting different lifespans and cancer susceptibility. Mouse, rat, and guinea pig genomes (short-lived and cancer-prone organisms) were compared with that of naked mole rat (Heterocephalus glaber) which is a cancer-resistant organism and the rodent with the longest lifespan. The long-lived bats of the genera Myotis, Rhinolophus, Pteropus and Rousettus were instead compared with Molossus molossus, which is one of the organisms with the shortest lifespan among the order Chiroptera. Despite previous hypotheses stating a substantial tolerance of TEs in bats, we found that long-lived bats and the naked mole rat share a marked decrease of non-LTR retrotransposons (LINEs and SINEs) accumulation in recent evolutionary times.
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| 19. |
- Ricci, Marco, et al.
(author)
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Transposable Elements Activity is Positively Related to Rate of Speciation in Mammals
- 2018
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In: Journal of Molecular Evolution. - : Springer. - 0022-2844 .- 1432-1432. ; 86:5, s. 303-310
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Journal article (peer-reviewed)abstract
- Transposable elements (TEs) play an essential role in shaping eukaryotic genomes and generating variability. Speciation and TE activity bursts could be strongly related in mammals, in which simple gradualistic models of differentiation do not account for the currently observed species variability. In order to test this hypothesis, we designed two parameters: the Density of insertion (DI) and the Relative rate of speciation (RRS). DI is the ratio between the number of TE insertions in a genome and its size, whereas the RRS is a conditional parameter designed to identify potential speciation bursts. Thus, by analyzing TE insertions in mammals, we defined the genomes as "hot" (high DI) and "cold" (low DI). Then, comparing TE activity among 29 taxonomical families of the whole Mammalia class, 16 intra-order pairs of mammalian species, and four superorders of Eutheria, we showed that taxa with high rates of speciation are associated with "hot" genomes, whereas taxa with low ones are associated with "cold" genomes. These results suggest a remarkable correlation between TE activity and speciation, also being consistent with patterns describing variable rates of differentiation and accounting for the different time frames of the speciation bursts.
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| 20. |
- Robert, Alois, et al.
(author)
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Digest : Population genomics reveals convergence toward melanism in different island populations
- 2021
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In: Evolution. - : John Wiley & Sons. - 0014-3820 .- 1558-5646. ; 75:6, s. 1582-1584
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Journal article (other academic/artistic)abstract
- Distinct traits between mainland and island populations provide an excellent opportunity to study the evolution and genetic basis of these traits. In this issue, Walsh et al. unraveled the evolution of black plumage color that arose independently in two island populations of the white-winged fairywren. They also described the first steps in understanding the genetic underpinnings of this trait.
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| 21. |
- Thörn, Filip, 1992-, et al.
(author)
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Contemporary intergeneric hybridization and backcrossing among birds-of-paradise
- 2024
-
In: Evolution Letters. - 2056-3744.
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Journal article (peer-reviewed)abstract
- Despite large differences in morphology, behavior and lek-mating strategies the birds-of-paradise are known to hybridize occasionally, even across different genera. Many of these bird-of-paradise hybrids were originally described as distinct species based on large morphological differences when compared to recognized species. Nowadays, these specimens are generally recognized as hybrids based on morphological assessments. Having fascinated naturalists for centuries, hybrid specimens of birds-of-paradise have been collected and the specimens kept in Natural History Collections. In the present study, we utilize this remarkable resource in a museomics framework and evaluate the genomic composition of most described intergeneric hybrids and some intrageneric hybrids. We show that the majority of investigated specimens are first-generation hybrids and that the parental species, in most cases, are in line with prior morphological assessments. We also identify two specimens that are the result of introgressive hybridization between different genera. Additionally, two specimens exhibit hybrid morphologies but have no identifiable signals of hybridization, which may indicate that minor levels of introgression can have large morphological effects. Our findings provide direct evidence of contemporary introgressive hybridization taking place between genera of birds-of-paradise in nature, despite markedly different morphologies and lek-mating behaviors.
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| 22. |
- Weissensteiner, Matthias H., et al.
(author)
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Discovery and population genomics of structural variation in a songbird genus
- 2020
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In: Nature Communications. - : NATURE PUBLISHING GROUP. - 2041-1723. ; 11:1
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Journal article (peer-reviewed)abstract
- Structural variation (SV) constitutes an important type of genetic mutations providing the raw material for evolution. Here, we uncover the genome-wide spectrum of intra- and interspecific SV segregating in natural populations of seven songbird species in the genus Corvus. Combining short-read (N = 127) and long-read re-sequencing (N = 31), as well as optical mapping (N = 16), we apply both assembly- and read mapping approaches to detect SV and characterize a total of 220,452 insertions, deletions and inversions. We exploit sampling across wide phylogenetic timescales to validate SV genotypes and assess the contribution of SV to evolutionary processes in an avian model of incipient speciation. We reveal an evolutionary young (similar to 530,000 years) cis-acting 2.25-kb LTR retrotransposon insertion reducing expression of the NDP gene with consequences for premating isolation. Our results attest to the wealth and evolutionary significance of SV segregating in natural populations and highlight the need for reliable SV genotyping.
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| 23. |
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| 24. |
- Xu, Luohao, et al.
(author)
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Dynamic evolutionary history and gene content of sex chromosomes across diverse songbirds
- 2019
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In: Nature Ecology & Evolution. - : NATURE PUBLISHING GROUP. - 2397-334X. ; 3:5, s. 834-844
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Journal article (peer-reviewed)abstract
- Songbirds have a species number close to that of mammals and are classic models for studying speciation and sexual selection. Sex chromosomes are hotspots of both processes, yet their evolutionary history in songbirds remains unclear. We characterized genomes of 11 songbird species, with 5 genomes of bird-of-paradise species. We conclude that songbird sex chromosomes have undergone four periods of recombination suppression before species radiation, producing a gradient of pairwise sequence divergence termed ‘evolutionary strata’. The latest stratum was probably due to a songbird-specific burst of retrotransposon CR1-E1 elements at its boundary, instead of the chromosome inversion generally assumed for suppressing sex-linked recombination. The formation of evolutionary strata has reshaped the genomic architecture of both sex chromosomes. We find stepwise variations of Z-linked inversions, repeat and guanine-cytosine (GC) contents, as well as W-linked gene loss rate associated with the age of strata. A few W-linked genes have been preserved for their essential functions, indicated by higher and broader expression of lizard orthologues compared with those of other sex-linked genes. We also find a different degree of accelerated evolution of Z-linked genes versus autosomal genes among species, potentially reflecting diversified intensity of sexual selection. Our results uncover the dynamic evolutionary history of songbird sex chromosomes and provide insights into the mechanisms of recombination suppression.
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