| 1. |
- Bergero, Roberta, et al.
(author)
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Meiosis and beyond - understanding the mechanistic and evolutionary processes shaping the germline genome
- 2021
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In: Biological Reviews. - : John Wiley & Sons. - 1464-7931 .- 1469-185X. ; 96:3, s. 822-841
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Research review (peer-reviewed)abstract
- The separation of germ cell populations from the soma is part of the evolutionary transition to multicellularity. Only genetic information present in the germ cells will be inherited by future generations, and any molecular processes affecting the germline genome are therefore likely to be passed on. Despite its prevalence across taxonomic kingdoms, we are only starting to understand details of the underlying micro-evolutionary processes occurring at the germline genome level. These include segregation, recombination, mutation and selection and can occur at any stage during germline differentiation and mitotic germline proliferation to meiosis and post-meiotic gamete maturation. Selection acting on germ cells at any stage from the diploid germ cell to the haploid gametes may cause significant deviations from Mendelian inheritance and may be more widespread than previously assumed. The mechanisms that affect and potentially alter the genomic sequence and allele frequencies in the germline are pivotal to our understanding of heritability. With the rise of new sequencing technologies, we are now able to address some of these unanswered questions. In this review, we comment on the most recent developments in this field and identify current gaps in our knowledge.
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| 2. |
- Borodin, Pavel, et al.
(author)
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Mendelian nightmares : the germline-restricted chromosome of songbirds
- 2022
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In: Chromosome Research. - : Springer Nature. - 0967-3849 .- 1573-6849. ; 30:2-3, s. 255-272
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Research review (peer-reviewed)abstract
- Germline-restricted chromosomes (GRCs) are accessory chromosomes that occur only in germ cells. They are eliminated from somatic cells through programmed DNA elimination during embryo development. GRCs have been observed in several unrelated animal taxa and show peculiar modes of non-Mendelian inheritance and within-individual elimination. Recent cytogenetic and phylogenomic evidence suggests that a GRC is present across the species-rich songbirds, but absent in non-passerine birds, implying that over half of all 10,500 bird species have extensive germline/soma genome differences. Here, we review recent insights gained from genomic, transcriptomic, and cytogenetic approaches with regard to the genetic content, phylogenetic distribution, and inheritance of the songbird GRC. While many questions remain unsolved in terms of GRC inheritance, elimination, and function, we discuss plausible scenarios and future directions for understanding this widespread form of programmed DNA elimination.
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| 3. |
- Kapusta, Aurelie, et al.
(author)
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Evolution of bird genomes-a transposon's-eye view
- 2017
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In: Annals of the New York Academy of Sciences. - : WILEY. - 0077-8923 .- 1749-6632. ; 1389:1, s. 164-185
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Research review (peer-reviewed)abstract
- Birds, the most species-rich monophyletic group of land vertebrates, have been subject to some of the most intense sequencing efforts to date, making them an ideal case study for recent developments in genomics research. Here, we review how our understanding of bird genomes has changed with the recent sequencing of more than 75 species from all major avian taxa. We illuminate avian genome evolution from a previously neglected perspective: their repetitive genomic parasites, transposable elements (TEs) and endogenous viral elements (EVEs). We show that (1) birds are unique among vertebrates in terms of their genome organization; (2) information about the diversity of avian TEs and EVEs is changing rapidly; (3) flying birds have smaller genomes yet more TEs than flightless birds; (4) current second-generation genome assemblies fail to capture the variation in avian chromosome number and genome size determined with cytogenetics; (5) the genomic microcosm of bird-TE "arms races" has yet to be explored; and (6) upcoming third-generation genome assemblies suggest that birds exhibit stability in gene-rich regions and instability in TE-rich regions. We emphasize that integration of cytogenetics and single-molecule technologies with repeat-resolved genome assemblies is essential for understanding the evolution of (bird) genomes.
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| 4. |
- Stöck, Matthias, et al.
(author)
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A brief review of vertebrate sex evolution with a pledge for integrative research : towards 'sexomics'
- 2021
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In: Philosophical Transactions of the Royal Society of London. Biological Sciences. - : Royal Society. - 0962-8436 .- 1471-2970. ; 376:1832
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Research review (peer-reviewed)abstract
- Triggers and biological processes controlling male or female gonadal differentiation vary in vertebrates, with sex determination (SD) governed by environmental factors or simple to complex genetic mechanisms that evolved repeatedly and independently in various groups. Here, we review sex evolution across major clades of vertebrates with information on SD, sexual development and reproductive modes. We offer an up-to-date review of divergence times, species diversity, genomic resources, genome size, occurrence and nature of polyploids, SD systems, sex chromosomes, SD genes, dosage compensation and sex-biased gene expression. Advances in sequencing technologies now enable us to study the evolution of SD at broader evolutionary scales, and we now hope to pursue a sexomics integrative research initiative across vertebrates. The vertebrate sexome comprises interdisciplinary and integrated information on sexual differentiation, development and reproduction at all biological levels, from genomes, transcriptomes and proteomes, to the organs involved in sexual and sex-specific processes, including gonads, secondary sex organs and those with transcriptional sex-bias. The sexome also includes ontogenetic and behavioural aspects of sexual differentiation, including malfunction and impairment of SD, sexual differentiation and fertility. Starting from data generated by high-throughput approaches, we encourage others to contribute expertise to building understanding of the sexomes of many key vertebrate species.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 I)’.
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| 5. |
- Suh, Alexander
(author)
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The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves
- 2016
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In: Zoologica Scripta. - : Wiley. - 0300-3256 .- 1463-6409. ; 45, s. 50-62
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Research review (peer-reviewed)abstract
- Birds have arguably been the most intensely studied animal group for their phylogenetic relationships. However, the recent advent of genome-scale phylogenomics has made the forest of bird phylogenies even more complex and confusing. Here, in this perspective piece, I show that most parts of the avian Tree of Life are now firmly established as reproducible phylogenetic hypotheses. This is to the exception of the deepest relationships among Neoaves. Using phylogenetic networks and simulations, I argue that the very onset of the super-rapid neoavian radiation is irresolvable because of eight near-simultaneous speciation events. Such a hard polytomy of nine taxa translates into 2 027 025 possible rooted bifurcating trees. Accordingly, recent genome-scale phylogenies show extremely complex conflicts in this (and only this) part of the avian Tree of Life. I predict that the upcoming years of avian phylogenomics will witness many more, highly conflicting tree topologies regarding the early neoavian polytomy. I further caution against bootstrapping in the era of genomics and suggest to instead use reproducibility (e.g. independent methods or data types) as support for phylogenetic hypotheses. The early neoavian polytomy coincides with the Cretaceous-Paleogene (K-Pg) mass extinction and is, to my knowledge, the first empirical example of a hard polytomy.
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